Try the Sopranos
Why have the standard (and IMHO boring and unrealistic) monolithic "City Sponsored Guild of Thieves and Assassins"?
Why not model your criminal organizations on real world or fictional mafia families and gangs. Maybe one city has two gangs (or guilds if you like the term) that are vying for control of the underworld.
One of them controls the docks and is really a gang of thugs held together by a charismatic individual (Rog/Sor x/y). Initiation into the gang is a ritual hit on their uptown rivals. They're mostly into smuggling, drugrunning, and protection rackets but since most of them have no qualms about killing (and everyone in the docks is too afraid of them to go to the Watch) a few coins in the right hands can get one or two of them to kill someone you don't like.
The rival group is a more organized bunch. Centered in the Artisan's quarter, the Guild of Torchbearers has managed to corner the market on crime. They have the formal structure of a Guild (ruled by a grandmaster with a number of masters, journeymen, and apprentices).
They got their start when the current grandmaster Tony (rog x/ftr y/ari z) got some of his friends together and started fixing prices for carrying torches through the city for nobles. As their plan initially met with some success, he cracked down on anyone who tried to offer their services at lower prices. He found a detective or two willing to look the other way for the right price and pretty soon, busted kneecaps kept all the torchbearers that weren't part of the guild from working.
With the guard in his pocket and a legitimate reason to be on the streets at night, Tony realized that he had the opportunity to burgle a few stores without getting caught. With the watch still looking the other way, Tony offered some merchants in the poorer quarters the services of his torchbearers--for a price. After all, if the torchbearers waited for customers outside their shops, they'd see if anyone burgled them. So now Tony's doing protection rackets as well.
With all the money coming in from his torchbearing monopoly and the protection racket, Tony went to the market and bought some slave girls to open a brothel (if prostitution is legal but disreputable--if it's not legal in the city, he opens a restaurant, bathhouse or massage parlor which everyone knows is really a house of prostitution but the watch never finds any evidence (it's hard to see evidence when you're distracted by gold)). His wealth has also made it possible for him to aquire rare (and illegal) items for his friends.
Of course, some members of Tony's guild--particularly his enforcers--can be hired to do a little freelance work. Even Assassinations. Tony will use his connections to protect them until they get to be too much trouble then he gives them to the watch in pieces as a present.
Recently, the dock gang started strongarming some of the merchants who're paying Tony for protection. Tony didn't appreciate them moving in on his territory and sent them a message. Since then the dockside boyz and the Lamplighters have been engaging in an increasingly violent conflict which is public enough that the watch may soon be forced to take action.
I don't know if that's what you're looking for but it's pretty easy to flesh that out. I'll suggest 3 levels for the NPCs depending on how you want the players to interact with the guild (low level members/enemies, up and coming members/enemies, or serious threat/leadership)
If you don't want to tailor the "guilds" to the plotline, just treat X as 3.
For simplicity, all the members are single-classed except their leaders so you can just use the generic NPCs from the DMG.
I would expect the total number of members to be adjusted to the campaign location but, assuming a fairly large city, it wouldn't be unreasonable to give the lamplighters a total membership of 75 and the Dockside Boyz a total membership of 50.
X=PC level
Dockside Boyz:
Leader=Sor/Rog Total levels=X+7/X+4/X+2
Inner Circle=Rog or Brb (possibly one clr of a chaotic god) Total levels X+4/X/X-2
Run of the mill thugs= Brb or War Total levels X/X-2/X-4
New initiates= Rog or War Total levels X-1/2/2
Lamplighter's Guild
Tony= Ftr/Rog/Ari Total levels=X+9/X+5/X+3
Masters=Rog or Ftr (maybe 1 or 2 Wiz) Total levels X+7/X+4/X
Chaplain=Clr (either Hextor, Zilchus, Olidammara, Sharess or some other god depending on how you want to play the guild) X+7/X+4/X
Journeymen= Rog or War (or Brb/Rog) X+3/X/X-2 to X-4
Apprentices= Rog, Brb, or War X/X-2/X-6