I'm currently trying to work out a specialized city personal guidelines myself. So far I'm trying to work with the basic precepts of having a commerce city, hammer city, science city, and a happiness/wonders/misc city.
That being said I look for a good location and then I try to find 2-3 nodes that will benefit the style of the city. Science cities want a lot of population growth so in the plains is a good start to look and find sheep/cows/whatever and then I build farms around it in empty hexes. A swamp nearby is also a bonus as it boosts your university if you don't chop it down.
A commerce city is normally a port city, hopefully near gold/silver for a mint, and surrounded by trading posts.
The production city is easy. You just find the hilliest spot you can find, hopefully with a bunch of hammer nodes, and you surround it with mines.
Now the key is finding a friendly maritime city state. Unless you just get super lucky on your commerce and production cities they'll be starving for food sources. Befriending a friendly maritime city state provides you with much needed food to populate.
The part where I'm struggling with this is finding a proper balance of population to happiness and what order to do the cities in. I find if I do production and science first I'm hurting on money which limits expansion. If I do a commerce city first it's a slower start and I don't feel established until almost post-classical.
Also I try to limit myself to 4-5 cities for culture reasons. Depending on the civ I'm playing I like to at least be able to fill out 10 policies by the renaissance. Generally I'll do tradition or honor and then commerce and then enlightenment. Commerce being the bread and butter.