First off, T2K has the strongest library of modules available for any game system. I have run Free City of Krakow about 7-8 times, and each time it played out in a different way, but was a blast every time.
My personal favorite is Armies of the Night. This is an absolutely epic module, that has ground down every PC group that I ran it with. Dozens of heavily armed factions determined to survive at any cost, a small mountain of gold, and an entire city to search makes for unstoppable fun.
I think I put this in another thread, but I remember it taking weeks (game time) to travel just a mile or so in Manhattan.