Am I correct in assuming the average guild isn't classy enough to be a Mystery? Making every single worker's union seems to cheapen the name. The Dockworker's Mystery would be funny the first time, but after dealing with a large number of similar orders the appeal would fade.
Now, mind you, there should be some form of thieve's guild (preferably dealing in everything illegal), some form of spy brotherhood, and some sort of scholar's gathering. Merchants, though, just don't have the secrets needed. On the spy brotherhood, though, I'd suggest making it so that the organization as a whole is strictly neutral, especially when it's members are in conflict with each other. So two rival lordlings might have spymasters who are both part of the brotherhood, and while they can call on the brotherhood for most things, the brothers will do diddlysquat against another member.