For level 1 cities, focus on basic production structures (workshops, logging camps if you're near a forest) and basic unrest reduction (bell towers, clerics if you have essence). It won't hurt to also build a basic income structure or research structure, but it isn't necessary.
When the city reaches level 2, you can specialize the city as a Town (gold income), Conclave (research), or Fortress (troops and imperial defense). If you choose for your city to become a Town, focus primarily on income structures and food structures. If you choose for your city to become a Conclave, focus on research structures and unrest reduction structures. If you choose for your city to become a Fortress, focus on production structures and unrest reduction structures.
Towns don't really need unrest reduction structures except for speeding construction - gold income is unaffected by the unrest level in a settlement, while research and production are - so for Towns a simple Bell Tower or a Cleric are probably all you'll need in the early game. You can add more advanced unrest reduction structures later, once your empire starts growing larger, or if you decide to build research structures in your Towns. You want your Towns to start producing Wealth once they have a few good income structures up (markets, merchants, tax offices if you have them), although if you have lots of low-grain cities then getting the Grocer line of buildings up fast is a good idea; higher level Towns also have some good bonus structures with faction-wide bonuses, so boosting the local food supply with the Well line and Garden line structures is a good idea. Local production is kind of irrelevant for Towns, although it helps for building the other structures rapidly, and Conclaves are better for research purposes. Also remember that a couple of world wonders (Merchantcross Bazaar and Treasury Vault) can only be built in Towns.
Conclaves should always get the research production buildings (remember that the upgrades to the Herbalist can eventually provide research and production, so don't forget to build that), so the standard research structures and the Sage line of buildings are priorities, and the Herbalist line of structures shouldn't be forgotten if your Conclave has essence or you need mana. Unrest reduction is very important in Conclaves, since the research output of the Conclave is multiplied by (100 - unrest)/100. Food and production are lower priorities, while income generation is better left to Towns since Conclaves can only build Merchants.
Fortresses should always prioritize the unrest reduction structures and the production structures. The special Fortress structures which benefit troops trained at that location are a priority for your primary training fortresses (which should also have high essence - three or four is good, if you can find a tile for it, although two is acceptable; also try to get at least 3 materials on a tile for a troop-producing Fortress). Any other Fortresses can ignore the special troop improvement structures, though if they are placed for map control you should probably prioritize city wall improvements. Food production is a secondary concern for Fortress structures; if you've already built the unrest reduction and production structures, and the troop enhancement or city defense structures, and are not training troops at the moment, build food structures, but otherwise food structures can wait. All other structures can be ignored, though if you don't have anything better to build you might as well build them.
As for balancing between the city types: it has been suggested that for every seven cities you build, four be Towns, two be Conclaves, and one be a Fortress. I would suggest that your first few cities be Towns and Conclaves unless you find a really nice spot for a Fortress early on, or are playing on a small map or against a large number of AI factions. If you haven't found a good fortress location by the time you've run into an AI faction or two, or by the time you've settled your fifth or sixth city, I would strongly consider putting a Fortress on the tile with the highest materials you can find, and building it up for troop training. If you have a choice between a 1/6/0 and a 4/4/0, I would put the Fortress on the 1/6/0, since with a few Towns up you'll probably only need a Garden to reach level 2 on a 1/6/0, and it will produce things 50% faster than the 4/4/0 (possibly even faster than that, since 1/6/0 tiles tend to be found in or near forests, while 4/4/0 tiles can sometimes be found in open plains). If you can get a site with fewer materials but which also has essence, that could also be a good spot, although if it's only one essence it might be better just to use the 1/6/0 site.
When choosing city tiles, also remember to check what strategic resources are nearby - gold mines make great sites for Towns, Wild Wheat resources mean you can choose tiles with only one or two grain but which have better material or essence values than other more fertile tiles in the area without suffering a significant penalty (at least once you've built on the Wild Wheat), Clay Pits mean the same thing for the material count of the city and can additionally make certain sites really good for Fortresses; additionally, things like Wild Game, Elemental Shards, Iron and Crystal Mines, or mount resources can be important for shaping your research and troop strategies. The shape of the map can also be important; I might choose to forgo a 4/4/0 in favor of a 3/2/0 if the 3/2/0 can block a pass in a mountain chain or cut off a peninsula, and places where forests and rivers come within a tile of one another can allow cities to construct both the Pier line and the Logging Camp line of buildings, both of which are fairly useful. Remember to look around the area where you are placing a city to make sure that you won't be releasing monsters you can't deal with (preferably, you'd wipe out the monsters in the area before settling, but that isn't strictly necessary) and that you aren't giving up really great city locations for no good reason. Don't settle a spot as soon as you find it just because it's settleable; scout around so you know what's on the tiles six or seven moves away (or even further) in all directions, then decide on a spot, unless it's a race between your pioneers and AI pioneers to get the area.
