As long as I dont use a lot of assassins:

One maxed out Merchants guild, ideally as close to the profitable resources as possible.
One maxed out Explorers guild (global movement bonus?).
One maxed out Theologicians guild (once it hits max level your priests get a significant global piety bonus, there's no need for more than one even if you recruit priests elsewhere, as your priests dont compete with others the way merchants do).
Knightly orders in the remaining cities (though this gets boring from a RP view), lvl 1 is enough.

I wouldnt actively work to get a thieves guild as it is very very easy to train thieves manually.

Swordsmiths guild in every castle (maxed out if non-Scottish catholic, otherwise level 1 is fine). Level 2 and above gives a global experience to knights, and this stack.

If muslim or byzantium I try to get a horse breeders guild (tricky as Byz, the easiest way is to capture a place with a horse racing track) for a global cavalry bonus, otherwise I dont bother with that guild.

Never had a woodsmans guild as I dont play the English, and never accept masons guild due to the relatively uninteresting bonuses.