I actually use different builds depending on the city's role, so I'll toss this out there for consideration:
Capital (town):
3) Grocer (10% HP)
4) Almshouse (+1 Prestige)
5) Mint of Ruvenna (+3g per mat)
This is because all the trades comes into this city, so I always specialize it as a gold producer (often has the treasury vault). Arcane Forge and Propaganda enchantment if possible...
Troop Producer (fortress, duh):
3) Strike Garrison (Impusive)
4) Prison (10% empire wide unrest reduction, -1 growth)
5) Great Arena (+2 Atk and +3 HP for trained units)
More often than not, the Great Arena isn't even needed, you basically toss on all the fortress upgrade you have and the best troop enchantments (make sure to build on a 2+ essence tile, with decent mat) and pump troops...
Unrest Fortress (...):
3) Infirmary (+1 Growth, and heals units)
4) Prison (10% empire wide unrest reduction, -1 growth)
5) Onyx Throne (30% empire wide unrest reduction)
This fortress is mainly built to reduce unrest empire wide, usually on a high grain tile (little or no essence is fine), the main purpose is to rush to lv5, so the Infirmary is there to help with growth. It generally also get a bunch of outposts and consulates if I can't spare governors. Having this allows me to set tax at much higher values, producing gold to buy everything.
Research cities (conclave):
3) Oracle (+1 Essence)
4) Pyre of Anniellum(+3 mana, +1 fire)
5) Hedigah Bathhouse (-30% Unrest, +1 water)
Oracle is the only one important on this build, the extra essence allows you to get more research from alchemist and Revelation. The other two is really only there to power up spells. I might have a couple of these in a large map game, mainly to keep research at a decent pace as well as power up those fire spells and slow.
All other towns:
3) Grocer (10% HP)
4) Almshouse (+1 Prestige)
5) Guild Tribunal (+2 production per mat for all cities)
Basically my build for everything else. I still prefer Almshouse for lv4 because it keeps a large kingdom growing without needing to baby sit it with governors/consultates. Besides, I often just buy everything I need with gold, so the production doesn't really matter all that much. Having a bunch of towns along with an unrest fortress makes that possible.
No Scroll Scribe, and no Governor's Office in sight... so I don't see those as being defacto at all.