My friend, John, who runs all of our Shadowrun campaigns, has a couple binders worth of info, just printouts and handwritten notes on tablet paper. It always seemed to be a big mess, but I'm starting to think it's a good idea. John had one binder with just NPCs, plotlines, and houserules, and another with all of Atlanta mapped out, including various building maps he made on an architect program he has, (and photocopied published Atlanta stuff from his Shadowrun books). He always runs our games in Atlanta, and over the 2 several years long campaigns I was in, and a few he ran before I knew him, he had a ton of info. I'm actually kind of jealous ;).
I tend to use a published city (Waterdeep) over the last 5 or 6 years. But I also was horrible about keeping campaign notes. If I had kept the various maps and NPCs I used, I'd have a lot more stuff to work with when I start up again. Instead, I'm back to my copies of the published material. That leaves me with a lot of information, but it also doesn't really leave the city as "mine". I have used bits from CSIO, Marienburg, Ptolus, and other published cities as well, especially NPCs.If I'd kept a running folder, even with notes like "this PC from this book goes here", my version of Waterdeep would be much more interesting to me. I have a fair amount of this stuff still in my head, but I never wrote it down. Maybe I'll have to do that soon.