I use two tools. A hard-bound laboratory-style notebook with quad rule and numbered pages, and my laptop.
Most everything I need for a night's worth of gaming goes into the notebook... I like the quad rule for maps and hierarchical bullet-points, and I keep the margin free for making reference notes... page numbers, rules to review, Dragon mag#s, etc., so I know where to check a reference. EVERYTHING I write or type goes into the laptop, which I use a variety of folders and subfolders to organize. To prep for a night's game, I print out a session outline, short stat blocks for critters and NPCs if I need them, and a sort of "running plot summary" for myself so I know where I've been and where I'm going, and tape it all in to the notebook.
Oh, in the back of the notebook, I have a few pages dedicated to names for NPCs, inns, towns, places, etc. etc. Whenever I need one, I just flip back, pick one, and cross it off the list.