The PC's have angered a Sczarni gang in Magnimar. They kidnapped a low-life for a day and let them go, realizing it was mistaken identity & paying him off for their silence.
Thing is, the area they kidnapped the guy from was under the protection of the Sczarni Washside Wringers, and many neighbors who came to try and help the lowlife got knocked out and beat up by the PC's, so even though the freed guy is, "good," the Washside Wringers considers themselves humiliated.
The Sczarni gangs in Magnimar are more mob-protection, shakedown, blackmail and intimidation than murderers or assassins, so tone it to that.
Don't want anything major, just tweaks and hooks to put the fear of, "We know what you did, and when you least expect it..." to the PC's to keep them looking over their shoulders while they continue with the AP.
maybe have the gang in question leave a "message" in a place the pc's thought was safe. Perhaps they find a note pinned to the wall inside their bedroom with a dagger. Maybe they're walking down the way when they get "Reverse Pick pocketed" and have a similar note put inside their pocket. Finally if one of the pc's has an animal companion/familiar you could have the gang find, kill, and decapitate something of the same species and have them put its head in their bed.
Of course, obviously the pc's are going to want to know how this happened. Since this is just you planting an idea and has no ramifications against the pc's then if they ask just say whoever did it made their checks (Remember that the dm can roll behind the curtain if he wants, for both the pc and the npcs). You could also include several sneaky spells such as pass without trace, invisibility, levitate, and dimension door as a means for entry/exit without detection.
Just remember that some players might see this as a challenge. They may want to find and kill this gang, whether you allow this is up to you.
Building off of Grimserver's wonderful ideas, how about the Sczarni legitimately believe that due to the PCs actions, they are now in te gang's debt. Have them require the PCs to pull off some ethically questionable missions for the gang. perhaps it increases the gangs power or decreases legitimate power. You could even have the specific missions be completely innocent, but the reprocess ions of the missions be highly favorable to the gang. By the time te PCs have paid off their debt, te gang is almost 100% in control of Magnamar. They can either continue to hep the gang (maybe even have them start getting more violent and vivacious as they gain more power) or have them start to fight the gang and help a legitimate ruler come back into power.
For someone that can threaten the PC's covertly, a 'rules of the concrete jungle' style feral hunter might be interesting.
Mostly, I like the possibility of wildshape for covert operations (a wild minded hunter seems more likely to work with a big city gang than a druid). Who suspects the rats (when not in swarms)? Who can protect themselves from assassins the flit in as bluejays, and that then grow a super beefy arm holding a dagger?
Being the literal fly on the wall works great for information gathering, and I can see such a person being valuable for a blackmail operation. At least having such a person as a distant contact and occasional contractor has its value. I am just suggesting this as a useful chess piece to use in any attempts to threaten and control the PC's.
Well, I like the dead animal thing... the Diviner/Wizard of the group has an owl familiar; hanging a dead owl at the gate to the Pathfinder Lodge would be something!
And since the area they did their business is also run by a Black Marketeer, I can see their prices going up and up if anything is made available at all.
Great suggestions!