It gives a boost to spy recruitment. If you train a spy there, you get an extra trait (in addition to the NaturalSpySkill trait) bestowing the boost. I imagine the boost is bigger for the Master and Headquarters buildings (2/3?), although I haven't got them yet, so I don't know for sure.

I couldn't find any info on the Guilds either until I looked at the Planner chart you get in the Collector Edition, which has a nice rundown of all the Guilds.