Glad you liked the links.
Here's a repost of some advice from the DM Mastery list. Hope that you aren't the same fellow who posted over there this week.
Second the advice on Gangs of New York. Excellent movie. (This was in reference to someone else suggesting that the DM watch Gangs of New York to get ideas for city campaigns.)
When you run a city campaign, keep *careful* track of dates. Have a calendar and note down who goes where and when. PCs do split up, as was astutely observed earlier. They will start to make contacts and have meetings set up and they will forget. You don't have to give them reminders (though I do give one because they are not their characters), but note when they miss one. Important NPCs might be irritated if someone doesn't show.
Note down external events that impact a city and occasionally toss in a reminder. I'm running a city-based campaign now. There's trouble on the supply routes, so some things like the assassin's favorite food - dusk melons - have run short. These little touches foreshadow events and make it real.
Determine what type of patrols are about in which neighborhoods. For some reason, I seem to wind up with a lot of chase scenes. It's important to know who responds if anyone does. If there's rooftops involved, you can make building notes similar to NPC notes - how high is it, what type of roof is it, who lives there, is there anything on the roof, any connections to neighboring buildings, etc.
Keep a sheet on locations. Once you've established an NPC at a place, the place is going to stick in people's minds. You don't want to send them to Minotaur's antique shop, which is supposed to be in a swanky neighborhood, but then describe it as being in the Thieve's Quarter. You'll find a memorable location is often visited by the PCs simply because they remember it.
The PCs will probably have a home or place where they live. Avoid attacking them there until they get in really deep opposing a powerful faction. But make it come alive for them so it feels like home. Example: I have two PCs living in an apartment on the fourth floor in a run-down quarter of the city. One of them animated some thieves that they killed to act as servants. The next time someone came to the door and saw that, there was a little nervousness. But,
this contrasted nicely with the demon downstairs knocking on their door asking for some spare entrails.
When you yourself are in a city, take a moment to study the people and places around you. Even though modern cities have differences with medieval ones (size being a key change), there are still plenty of things to observe. There's monuments all over the place. Architectural styles mix it up as old buildings are remodelled and/or replaced with new. People interact on the streets and in the shops constantly. Trash accumulates in weird places. Life is different.
Mike Mearls has a pretty good book out called Cityworks. I've been going through it. It's got some good advice, so I recommend picking it up if you can.
Edit: fixed carriage returns