Basic Overview
First we need to go over the basics, terms and abbreviations so that everybody is on the same page. There are 3.5 types of specialized cities. I say 3.5 because a few of them are just a specialization of one. They are:
- Great Person Farm City (GP Farm)
- Production City
- Commerce Cities
- Scientific Commerce City
- Money (Gold) Commerce City
- Holy Commerce City
- Hybrid Commerce City
We will discuss each in detail later on. But the basic function of each is pretty self explanatory. GP Farms grow nothing but Great People. Production Cities make your defensive units. Commerce Cites make your money and science. The ratios of how many of each you need vary from player to player. Typically, only one GP farm is needed for the map, and a ratio of 2 production per 3 Commerce cities is sufficient. A lot of this depends on if you plan on being aggressive or scientific/cultural, and also how many of your commerce cities can double as production cities (called hybrids). You can get away with having just two pure production cities, but it helps to have more in war times. If you have a lot of hybrid cities (which you will), count them as both a Production and Commerce city, and still aim for the 2:3 ratio.
There are also a number of National Wonders that you can build to enhance your cities specialization. Most will probably go in Production cities, just because it’s quicker to build there. We’ll discuss which ones are useful for what cities when we get into the detail of each, but let’s list the wonders first. All Nation Wonders generate 1 Great Person Points, and the type it favors is listed in parenthesis:
- Forbidden Palace: (Merchant) Reduces maintenance in nearby cities
- Globe Theatre: (Artist) No unhappiness from this city. Can turn 3 citizens into artist
- Hermitage: (Artist) +100% culture in this city
- Heroic Epic: (Artist) +100% military unit production in this city
- Ironworks: (Engineer) +50% hammer with Coal. +50% hammer with Iron. Can turn 3 citizens into Engineer
- Mt. Rushmore: (Artist) -25% War unhappiness from all cities
- National Epic: (Artist) +100% Great People birth rate in this city
- Oxford University: (Scientist) +100% research in this city. Can turn 3 citizens into Scientist
- Red Cross: (Scientist) Free Medic I promotion for units built in this city
- Scotland Yard: (Scientist) Required to train Spy
- Wall Street: (Merchant) +100% gold in this city
- West Point: (Engineer) New units receive +4 experience points
Understanding Commerce Points versus Gold/Money
I needed to add this section, because even I was confused by it. Civ4’s use of Gold icons and terminology gets really confusing, so let’s explain it because it is critical to city development.
Commerce is the number of gold “coins” and money bags that appear in your city’s workable tiles. To prevent confusion, I’m just going to call these Commerce Points (which I’ll abbreviate to CPs). A coin equals 1CP and a money bag equals 5 CPs. Foreign trade routes also generate CPs (if somebody wants to explain how this works, please do). All of the CPs generated from your trade routes and tiles are added up and become your City’s total Commerce.
Gold or Money is what is generated after you take your CPs and put them on the Science/Gold/Culture Slider. Usually this is set to something like 90% Science, 10% Gold. So if your city generates 100 CPs and is put through the slider, you will get 90 science beakers and 10 actual Gold pieces of Money.
This is important to know because your city buildings effect what happens AFTER the CPs have gone through the slider. Building a bank will increase the Gold produced in the city by 50%, not the Commerce! So if your city makes 100 CPs and you put it through the 10% slider. You will wind up with 10 gold. Multiplied by the 50% bank bonus, you get 15 Gold in Money. You do NOT get 150 in Commerce Points.
Same thing with Science. Constructing buildings or wonders will increase the science output after it’s gone through the sliders.
Feeding your City
This part of the strategy was given to me by Wreck, so I can’t take credit for it. I will try and explain it though.
The key to getting your city to thrive is to give it just enough food improvements (farms) to grow to maximum size. Everything else is excess and will take away from the specialization. (The GP Farm is the exception)
Every population point in your city consumes 2 food. Fortunately, every population point (up to 20) provides a new worked space in your city’s fat cross (workable area around the city) and that in turn provides more food. When you start a city, you get 2 extra food from the city itself (called +2F) plus whatever food is in the first space highlighted or “worked”. Usually that is +2F or +3F as well. Ideally, if every square around your city was +2F (grassland), then your city would grow to full size, because every time your city would grow, a new worked spot would provide +2F to cover the -2F needed for the higher population. You would always have the +2F surplus that’s given to you when you start your city. (-2F for a population of one, with a +2F for one worked spot plus the +2F from the city itself)
I hope that makes sense! 
The problem is, you never have +2F in every square. When you start using areas with only one food (+1F) or no food, then your will start reaching a point where your city no longer grows, because you are eating into that initial +2F surplus you get when you start the city. To get back onto the plus side, you need to use tiles with extra food bonuses, like floodplains or resources … or build farms (which give +1F on top of your tiles normal production)
But you never want to build more farms than you need, or else you’re wasting tiles. Ideally, what you want to aim for is no food surplus when your city hits size 20. That way all tiles are being worked, and you don’t have to worry about growing any bigger … plus you have the maximum amount of tiles are being used for commerce and production. (Note: You will likely have a few cities with unworkable tiles like mountains or ice or worthless tiles like tundra. If this is the case then aim for a city size the is 20 minus how many ever tiles you plan not to work.)
So how to do this …
The first thing you need to do is count the number of extra food in your fat cross. Remember you get an extra +2F just from the city itself, so count that as well. Any tile that gives you more than 2 food, count as an extra +1F. A floodplain gives you +3F, so that’s +1F. Various resources will also give you bonuses. Count the extra amount of food given over 2. Don’t count bonuses given by creating a farm. This is just “as-is” bonuses.
Next you need to count the number of spots that have less than 2 food in them. Any Plains spots count as -1F. Deserts, Tundra and Mountains count as -2F. Jungles are a bit tricky, because they take away food bonuses. You should plan on chopping your jungle to make room for a cottage or mill, so count it as if it were normal grassland, hills or plains. (Note: If you are planning for a smaller city because of useless terrain, do not count the terrain you don’t plan on improving in your calculations)
Then combine your two numbers. If your number is 0 or greater you are in great shape. If it’s below zero, then you will know exactly how many farms you need to add to maximize your land.
So for example, if you have a city built with 6 plains spots, 1 floodplain, and every thing else grassland … Your extra count would be +2F (city itself) +1F Floodplain for +3F. Your losses would be -1F x 6 (6 Plains) for -6F. Everything else provides 2F, so they don’t effect the equation. Add the numbers, and you have a -3F shortage. Build three farms, and you are even. Everything else can go towards specialization.
Building farms on food resources where a farm is needed (corn/wheat/rice) is highly recommended, since it will give +2F on top of it’s initial value. That means you have one less farm to build elsewhere. Not to mention you also get the health bonus and resource as well.
Specialized City: The Great Person Farm
Now that you know how to optimize your city’s food … let’s look at the lone exception: The Great Person Farm. The sole purpose of the GP Farm is to generate a ton of Great Person points. One way to do that is to build wonders. But the other, easier way to do it is to have a ton of specialists. You can do that by having an extreme abundance of food.
This is usually the second city you build. You will want to find a nice grassy area, preferably with a river running through it and food resources nearby if possible. If you can get an area with some plains hills (2 or 3) in the corner, then even better. If you can get the area covered in forests, then you’re really in good shape. Some people would probably disagree with the hills, but I like to try and build wonders if I can get them, since it can’t hurt to have some extra GPP points coming in. Also it helps to have some extra production to build health and happiness when you need it.
To improve this area, you are looking at mostly farms. Farm the resources, floodplains and areas around rivers first. When you get a chance, mine the hills to get your production. Then go back and farm everything else.
The forests are very useful for pumping out World Wonders, which give you an extra +2 GP Points. You can try to build some of the earlier wonders and chop rush your forests to make room for your farms. You then get your Wonder bonuses and benefits, plus the GP Points you’ll need later.
As for National Wonders, National Epic and it’s +100% Great People birth rate is a no-brainer. The Globe Theater is a good one to build as well, as it will eliminate the unhappiness barrier you will constantly run into with your large population size. Some people like to build the Hermitage for it’s +100% Culture, but I’m not sure that it’s necessary unless you are going for a cultural win.
The City Buildings you build are only going to be the ones you need to boost happiness and healthiness. No need for banks or barracks or the like here. You just want to keep your large population happy and healthy as you will be brushing the maximum frequently.
The real trick to this city is watching the happy numbers and to a lesser extent the healthy numbers. You will usually gain a point every time your population goes up (and it will go up quickly). So the trick is to slam the brakes on population growth as soon as happiness equals unhappiness. Watch these number frequently, like every third turn or so. When you max out, switch your food squares to your production squares and build something to raise the maximum (temples, aqueduct, coliseum, etc). If there are no buildings available to help, then turn off your worked squares and convert them to specialists. You will want to stay at “stagnant” population growth until your maximum happy goes up again. Trading for resources can also help. If needed, use your “stop growth” button to keep from getting too big (Helpful if you have an odd number of food surplus) … but be sure to turn it back on when you can get bigger. Health is a different story. You can afford to get into the “unhealthy” state, but watch this closely as well, because an unhealthy city will start eating at your food surplus. If you get too unhealthy, your growth will become stagnant and you will be unable to switch over to production without going into negative growth.
Specialized City: The Production City
The Production City is primarily used to build your military units, but can also be used to to create some World Wonders late in the game. I’ve had a few good production cities end up becoming secondary Great Person farms, just because I was able to build so many world wonders in them. (Granted, this probably won’t work in higher difficulty, and it’s not recommended to do, since it will hurt the efficiency of your actual GP Farm) Still, this is where all your unit generation comes from. If you plan on being a war monger, you might want a few more of these cities than usual.
A production city should ideally be placed in a city with a lot of hill spaces, but also some grassland as well. An area with a lot of plains and forests will also work as well, although it will take awhile before you can build lumber mills. (Although the benefit of a forest space is that it can’t be pillaged!) The problem with a lot of hills is that unless they are grassland, you’re not going to get a lot of food to make your city grow. A hills/grassland combo works best, because you can grow farms on the flat areas and mines in the hills … and you will be able to use the mines almost right away.
To improve, you will want to get a farm or two going to get the population up. Then start a mine or two, and alternate back and forth as you grow. As you would expect, mine resources and farm food spots first. If you calculate out a surplus and have some extra grassland spots, save a few forests for production and make lumber mills later on. For plains terrain production cities, you will likely be building a lot of farms, but each farm will also give you +1P so the production will add up as you grow.
World Wonders are really up to you. If you choose to build any, these would be the cities to do it in. The Three Gorges Dam is a decent production-specific wonder as it will provide power to all your cities. The Kremlin is also nice, as it will be cheaper to rush units. If you get a few good production cities that can turn out units in 4 or 5 turns, you can pump out an army incredibly fast just by producing one turn, and buying the next.
National Wonders should go to your best production cities, and are usually better when paired up. National Epic and West Point are great to have together, as you will turn out some elite units very quickly. Iron Works paired with Red Cross works just as well to produce units quickly with an extra medic promotion. Scotland Yard can also be paired with Iron Works to make a lot of spies. Mount Rushmore is a good candidate to build in a production city, just because it will be built more quickly than in other cities, and it’s effects are felt everywhere.
Your city buildings are mostly going to be geared towards increasing production. However, with the added production, it will be fairly easy to build other improvements as well. Try to build forges, factories, etc as soon as the become available. Build Happiness and Health buildings when they are needed. Health is probably your main concern, since most production increasing buildings hurt health. Build military units the rest of the time. If you don’t plan on building a large army, then you can afford to build just about whatever you want here, because it will get done fairly quickly.
These cities usually aren’t as high maintenance as the GP Farm. Occasionally check in to see that your unhealthiness hasn’t exceeded your health maximum. (Otherwise your food calculations won’t work!) I usually concentrate on growth when I first start these cities, and then switch it off when it gets to a moderate city size. After that, the hammers will increase every time it grows, so there’s no real need to turn on the production emphasis. (Unless you want to hurry up and build a forge/factory/etc)
Specialized City: The Commerce City
The Commerce Cities are probably your most important city to have. Without it, you would be unable to support a military or research new technologies. The key to Commerce Cities are cottages, and building them as soon and as often as you can. Cottages only grow when they are being “worked” so it is important to monitor your food situation as well.
The ideal location for an Commerce City is just about the same as a GP Farm. A lot of grassland, a river touching a lot of squares, a couple of hills, and a number of resources. However, just about any area can be used to create an Commerce city. It’s all a matter of balancing your farms and cottages so that your food surplus hits +0F when your city size maxes out. If you are lucky, you will get an area with a lot of grassland (+2F) and you can just build all cottages. If you get a lot of plains, you might have to get a lot of farms to support your cottages. (Worst case scenario, you just make it a production city)
Improving your land just follows the “Feeding your City” section. Build just enough farms to stay in a surplus until city size 21, and then cottage everything else. I like to have a few hills in these cities because production will be awful here. Because you are aiming for flatland/grassland areas, you’re going to end up with all farms and cottages. Production needs to come from somewhere if you plan on having a bank, so it’s nice to switch to your hill spaces when it’s time to build something. As for cottages, aim for the floodplains first. They already give a +3F output, so building there means you get your food advantage, while having that cottage “worked” and growing. If you have an over-abundance of a resource, sometimes it’s better to cottage the space and reap the tile benefits while growing the cottage. Mature cottages will generate a lot more cash than the fixed income a camp or plantation will give you. Also try to build on rivers if you can (you may need them for farms), because the river provides some extra commerce.
You may end up changing your improvements a lot in these cities. Start with mines on your hills to begin with, but change them windmills later on. When you get the +1F per square from Biology, you can also turn a lot of farms into cottages. Don’t be afraid to throw cottages on your grassland hills either.
World Wonders are a little tough to build here, because you are sacrificing production for commerce. If you can, chop rushing something like the Great Lighthouse or Colossus early on can be beneficial to generate Commerce from water spaces. If you have a lot of trees early on to waste, then you can consider rushing another wonder, but usually these are best left for the production cities.
National Wonders and City Buildings depend on which of the four kinds of Commerce Cities you plan to build. More on these in a bit
Monitoring these cities is a little more difficult than production. Depending on what you are building, you may need to switch over to production-heavy squares when needed. Try to always keep your cottages “worked” or they will not grow. These spots should get preference over anything else. Emphasizing Commerce is probably a good way to go.
Specialized Specialized City: The Scientific-Commerce City
Balancing you Science Commerce cities and Money Making Commerce cities is key. I usually use my best or two best Commerce producers as Science Cities and use all the rest as Money Making Commerce. With a lot of Money Making Cities and Universal Suffrage, I’m able to buy just about anything I need later in the game.
Science Commerce Cities are usually my best Commerce Cities (check the beaker counts in each city). The only difference is, you want to specialize in a lot of science buildings if you can. Because there are your best Commerce cities, production will likely be very low. Try to concentrate on science buildings like Libraries/Universities/Labs/etc first, and Happy and Health Buildings only when you need them. Try to save any forests you have for chop rushing Oxford University. The +100% science is a huge boost to have in your best science city. If you get a Great Scientist, build an Academy here as well.
Specialized Specialized City: The Money Making-Commerce City
Naturally, the best city buildings here are going to be banks, markets, grocers and the like. Anything that increases Gold/Money production. For your water cities, a lighthouse is a must. Once again, it’s going to be very difficult to create buildings here because of your loss of production. Aim for Money buildings as soon as they are available and try working on Happiness and Health building the rest of the time.
Specialized Specialized City: The Holy-Commerce City
These are cities that are fortunate enough to found a religion. As soon as you get a Great Priest, build that religions special building and get your religion spread. With the proper civics, you will generate a ton of Money from other cities using your religion.
The best city building improvements here are going to be the same as a Money Making City: banks, markets, grocers, etc, but also the Holy buildings as well. The Temples and Churches should aid your happiness numbers, so you should only check in with your health numbers occasionally to make sure it isn’t killing you.
The best National Wonder you can build here is Wall Street, which provides you with 100% Gold. Unless you happen to have another Money Making City that’s generating more Gold/Money.
Specialized Specialized City: The Hybrid-Commerce City
These are cities that are basic Commerce City, but also have a lot of production to go along with it. Because most of the cities you create need to be Commerce cities, you wind up with a lot of cities on plains or hills or in a nice mix of terrain. I just count these as both a Production and Commerce city, although it won’t be as efficient as a purely specialized city.
Because Commerce is most important, treat this city like a Commerce city. Build cottages where you can, and farm, mine and windmill the rest. If you follow the “Feeding your City” section, you will wind up with a city that has a couple of cottages generating some money, but a lot of added production to boot. This is helpful in times of war when you need a couple different cities turning out units.
But as I said, treat this as a Commerce city, first and foremost. The production bonus is more of a by-product of the terrain.