You can't have just one, cause they're always going to have competition...
Anyway, I recently went with a very "traditional" Thieve's Guild - Wererats. Yeah, I know, overdone. But it just fit the feel at the moment (they were at war with a different Thieve's guild run by a very slippery little kobold that was sort of like the "yoda" of rogue's, heh.)
At any rate, the wererat gang was separated into different groups, each with it's own leadership and all organized under one ruthless "boss". Each group had different functions for the clan as a whole and members were tattooed with unique markings as per their role with the gang.
The Empty Purse (Pick Pockets - a cutpurse emptying into a fat rat's mouth)
The Plague (Extortion - black rat with hapless humanoid by the err...privates)
Tunnel Rats (Burglary - rat dragging goods into a hole)
"Cheese" Brokers (Illicit Drugs - rat reclining with large water pipe in front)
The Swarm (Eyes and ears - street scene with hidden rats)
Bodyguards generally had a tatt of a Muscled rat with a severed cat's head in its mouth
Not every member was a wererat. In fact, most weren't, however some aspired to be wererats and the leadership was made exclusively of the creatures.
They would generally attack only if they had superior numbers, utilized swarms and hordes of rats readily available in the sewers as fodder (through spells and other abilities), and were generally ruthless and highly territorial.
General combat methods included lots of mobility (spring attack and the like) and use of their hybrid forms where in the sewers they could use their Climb speed to attack from nearly any angle. A swarm of these guys charging down a narrow sewer tunnel along every available plane (top, bottom, sides) was generally unsettling for the players.
The main leader was a rogue / sorcerer who was fond of fear spells, summoning swarms of rats, and paralyzing his foes while feeding them to said swarm of rats (this was inspired by an actual mafia hit man who seriously did that to people with paralytic drugs and a video camera to record the event - yeah the above note about looking into real world stuff is spot on...and more creepy than DnD ever thought to be...) All of his spells centered not so much around damage but just messing with his opponents ability to well, do anything (fear, blindness, paralyzation, etc.) .
One of their bases was an abandonded elven monastery on a hill in the poorer part of town. The rapidly expanding city and the subsequent attempts to create a sanitation system for the growing population had led to an enormous sinkhole near the monastery (which of course fed into the sewers.) The site had thus been abandoned (well, and the "foreigners" were all sort of forced into one Ward of the city as well...long story). The bell tower of the monastery and the fact it was siutated on a hill, gave for a great lookout post for the Rats.
They had a "pet" monstrous centipede in the basement which they kept at bay with "food". The monastery itself was largely run down and they held busines meetings in the "Chapel" area. A well in the courtyard provided yet another access to the subteranean world.
I don't have any of the notes and such in front of me and my lower powered games might not provide you with the type of stats you are looking for, so they might be of limited use. For the monastery base I mentioned I used a modified version of this map:
Medieval Monastery Map
Hope that gets your creative ideas flowing!