Red Wizards of Thay from FR, as revised in the 3.x FRCS. I'm pretty sure that an evil magocracy that's trying to expand its influence through the sale of magic items and contraband can fit in any campaign.
Eldreth Veluuthra from FR. Nazi elves? Sold. I've always seen elves as arrogant bastards, and these guys really fit.
Churches of Malar, Tempus, Loviatar, Auril, Velsharoon from FR. Malar's church is filled with evil rangers who live for the hunt. Tempus promotes war as the best solution for all conflicts. Loviatar's church (of pain) is evil, but very much present (even officially so) in most cities, since young nobles love their little S&M games. Auril, the Frostmaiden, wants to enclose the world in ice and forever preserve it as it is. Velsharoon is the patron of undead who believes that only those who prove themselves are worthy of undeath; plus, he encourages... experimentation.
Sensates ("we want to experience all"), Fated ("we don't need your stinking help"), Mercykillers ("we will ensure that justice is served... no matter the cost"), and Dustmen ("true death waits for us all") from Planescape are great and I think they can be adjusted to work as guilds in any campaign setting.