Since there appears to be some confusion over the effects of the free buildings you get at various city levels:
- Archivist: +50% city research production when producing research here
- Oracle: +1 essence in city
- Scroll Scribe: +20% to city research production; provides Blizzard Scrolls, Return Scrolls, and Summon Air Elemental Scrolls to shop
- Academy of Revelation: +10% faction research production
- Amethyst Vault: +2 crystal production per season
- Tenfell University: this city's research production is unaffected by unrest
- Hedigah Bathhouse: +1 Water Mana; city unrest reduced by 30
- Pyre of Anniellum: +2 Fire Mana
- Tower of the Magi: trained units receive 10 extra spell resistance; city is immune to strategic spells
- Infirmary: units trained here receive trait "Endurance I" granting them an extra 1 health per level; units stationed in this city heal by an extra 10 health per turn
- Strike Garrison: units trained here receive the "Impulsive" trait, granting them +2 initiative
- Watchtower: units trained here receive trait "Charge" granting +1 move and +2 attack on their first turn in a battle; city defense force increased by 1 catapult
- Gallows: this city's production is unaffected by this city's unrest level
- Mining Guild: +2 metal production per turn
- Prison: -10 unrest in all the cities you control; -1 growth in this city
- Great Arena: units trained here receive +1 attack (note that this probably only applies to units with nonzero base physical attack) and +3 health (both of these apply per-figure)
- Onyx Throne: -30 unrest in all cities controlled by the player
- Underforge: +1 Earth Mana; armor production cost is halved in this city
- Guild Grocer: +5% health for all the player's units
- Slums: +3 growth in this city; +5 unrest in this city
- Guild Warehouse: +50% gildar production in this city when producing wealth here
- Almshouse: +1 Fame per season
- Embassy: the unrest penalty for empire size is negated in this city
- Governor's Office: +1 production per material in all cities of this player
- Guild Lendinghouse: +2000 gold upon construction; no ongoing bonus
- Guild Tribunal: +2 production per material in all cities of this player
- Mint of Ruvenna: +5 gold production per material in this city
Note that the Hedigah Bathhouse, the only 5th level Conclave improvement that affects unrest, only affects unrest within the city. You can check this yourself by finding CoreImprovements.XML and comparing the section which modifies unrest with the sections modifying unrest in the Gallows/Onyx Throne/Apiary and Bell Tower/Cleric/similar. Bell Towers and Hedigah Bathhouses and Clerics modify Unrest, Gallows and Onyx Thrones and Apiaries modify a player ability which affects unrest. The player ability is global, the unrest is local.
As for the actual topic of the thread:
I like to start off with a Conclave, followed by a couple of Towns and more Conclaves, with a Fortress coming out around the sixth or seventh city I build, unless I find a good Fortress site earlier (3+ essence preferred for my main training Fortress or Fortresses, none required for any of the others). I think a ratio of perhaps one Fortress per five or six other cities is reasonable; early in the game the other cities will be weighted more towards Conclaves, and later (when I'm satisfied with my faction's research production) the weight will shift towards Towns. Spellcasting-focused games should have more Conclaves, since Conclaves are the best mana sources other than shards. Army focused games should have more Towns to fund that army, and perhaps more Fortresses to produce it. Towns are by far the best type for money production, Fortresses are by far the best for elite troops (unless you really need the bit of spell resistance a Tower of the Magi can provide, but that's not that likely to be worthwhile) and generally better for fodder unit production, Conclaves are the best at research, but aren't terribly far ahead of Towns and Fortresses when you consider that instead of the build time for the Sage line you could have been using 'Produce Research') and by far the best at mana production. Additionally, if you're playing a resource-poor map, Conclaves and Fortresses can be used to partially make up for lacking Iron Deposits or Crystal Crags, though I prefer the choices over Mining Guilds and Amethyst Vaults most of the time.
As far as building up cities goes: I usually build workshop/bell tower/cleric/logging camp first in any city (as much of that as is available, anyways, and usually in order of what builds fastest). Other upgrades depend on what I want out of the city and what my empire currently needs, though production and unrest improvements are always useful if I'm going to be further improving the city or gaining research from it. You need to consider whether or not you think the game will last a while (more focus on city improvements, less focus on troops, though you might want to start building an elite corps), or a short time (more focus on troops, less focus on city improvement, and perhaps more focus on troop quantity than quality).
As for level-up choices in cities:
I like for Conclaves to have at least one of natural essence, an Oracle, or a Scrying Pool, because otherwise you can't upgrade the Herbalist or build Clerics. If it's predominantly a research city, I could go with either the Archivist or the Scroll Scribe, depending on the stage of the game - early game, I think the Scroll Scribe is better because it's always in effect, and it gives you access to some potent spell scrolls; later, it's a toss-up, though scroll access in a border zone is something that's worth considering. Third level Conclaves usually go for either of the research bonuses, favoring the +10% to the faction research if I have a well-developed or large empire, and favoring the no unrest penalty to research if my research production is highly concentrated. Amethyst Vaults aren't something I normally take, because usually by the time I get a fourth-level city I either have enough mines in my empire to meet my needs or I haven't researched enough of the magic tree to make it worthwhile because I didn't have a good crystal source. Fifth level Conclaves will always get one of the magic-boosting structures (Bathhouse or Pyre) because Spell Resistance, particularly in that low of an amount, isn't that useful and I don't really want to pass up on the Fortress troop bonuses. I favor Bathhouses in research cities if I don't have enough high level Fortresses to keep the unrest down, otherwise it depends on how many Fire/Water mana I currently have and how many Fire/Water spellcasters I have.
For third level fortresses, it depends on where the Fortress is and whether or not it's a border Fortress, as well as what kinds of troops I'm making. Infirmaries are tempting for border Fortresses if the border is likely to be stable since they can more rapidly restore an army to full strength; Watchtowers are tempting for less stable borders where I might need to rely partly on city troops to hold the border. Watchtowers and Strike Garrisons are good for aggressive troop designs and for making up for initiative penalties from armor or equipment, while Infirmaries are better with tank designs if you can keep the tanks alive to get to high levels. At fourth level, you have a choice between production, resources, and global unrest reduction. As with Amethyst Vaults, I don't find Mining Guilds generally useful for all the reasons given for Amethyst Vaults, with the added reason of Iron Deposits being generally more common and more productive than Crystal Crags are. Gallows are good for training Fortresses, Prisons are acceptable for non-training Fortresses as long as they can still grow even with the penalty or if the game wasn't going to last long enough for the growth penalty to matter much. Fifth level fortresses get Great Arenas or Underforges if they're training Fortresses, or Onyx Thrones for the Imperial Economy, or Underforges in the rare case that I want additional Earth Mana. I prefer Great Arenas to Underforges for training Fortresses, as the Great Arena makes the troops better whereas the Underforge just makes them train more rapidly, unless the fortress is a site for the training of heavily-armored disposable units.
For third level Towns, I will almost always take the Guild Grocer, with the exception that I'll have a Town or two with Guild Warehouses that I plan on making over into major money producers (best if they're near gold mines, have high materials, and have the Treasury Vault wonder). On the rare occasion that I plan a city for use to feed one of the sacrifice spells, I might choose a Slum, but that's rare. Fourth level towns almost always get Governor's Offices, because by the time a town attains its fourth level I rarely have a use for +1 Fame per turn (Almshouse), though if I'm playing with Henchmen/Sions or want to have as many champions as possible it might be a different story, and I don't usually need to build more stuff in the city or need much research from it (Embassy). Additionally, if I've got Towns approaching their fourth level, I should have Fortresses close to the same point, and Fortresses are in my opinion a better cure for faction-size unrest than Embassies are, because Embassies only affect the town they're in and yet I don't usually have anything affected by unrest in a Town, unless it's building its next money improvement (I don't usually build research structures in Towns unless I think the extra research would be useful, as Conclaves are a bit better at it and I would usually rather use 'Produce Wealth' in the Town, and I don't usually train anything out of a Town, either). Fifth level Towns either get Mints of Ruvenna, if they were selected as main money producers earlier (e.g. I chose Guild Warehouses) or if I really need an economic boost, or Guild Tribunals, with Guild Tribunals being generally my preferred choice. I don't think a once-off bonus of 2000 gold is sufficiently worthwhile, unless I'm absolutely desperate for money to rush something (or several somethings) out or desperately need money for outfitting a champion. By the time fifth level cities come into play, one-time money bonuses just aren't usually that helpful to me. If it had some other bonus attached (say, +10% faction-wide gold production, or +1% treasury interest, or something like that), I might consider it worthwhile.