The first thing to do is background work. Who are the movers and shakers, and what do they have going on, who are they allied with, and who opposes them. I generally make up about 20 frontline groups the PCs are likely to encounter. From Dwarven supremiscists up to the town guard.
Make templates of characters from various groups so you can throw one in with almost no notice.
Draw up stand alone maps for stock locations. You know, for instance, that the players are going to go into a seedy bar. Plan for it.
Make a list of names. When you need a name, grab it off the list. Note who you gave it to, and why they're important.
Now the fun part...
Urban adventures occur in vignettes. Don't put together an overarching adventure. Do short scenes. Like this:
The PCs are on top of a building (or somewhere else they can't leave quickly) see a richly dressed woman forced into a carriage, and the carriage leaves in a hurry.
Make a book of about thirty vignettes. You'll only use about five a game, but you want to have ones appropriate for any situation the characters find themselves in readily at hand. Replace them between games.
Keep track of the enemies they make.
Throw the PCs into the chaos. They'll start drawing connections. It's human nature. They couldn't avoid it if they wanted to.
Take their most evil ideas about "what's really going on", and incorperate them. But add a twist so that they *almost* figured out what was going on, but are still suprised. (Shoot for the reaction "I should have seen that coming!")
You're flying fast and loose, so have a prop to buy time when you need it. Something to drink works well, since you can't drink and talk at the same time, and since you're talking a lot, your throat will get dry.
Any source is good, be it WoTC, Paizo (Dragon/Dungeon or Gamesmastery) or other 3rd Party company. 
