I put all of my negatives in Print File sleeves and store each roll in a file folder along with a contact sheet, exposure notes and any work prints and printing maps that I have made from that roll. Everything associated with a roll of film is in the same place. The files are stored in an old steel filing cabinet. I also make a second contact sheet of each roll and store them in 3 ring binders to make finding specific rolls easier later on. I file rolls and contact sheets in chronological order which corresponds with my numbering system. I shot a roll yesterday which will be 2009-01-03-01 (year-month-day-first roll shot that day).
I wonder, though, why I cannot bring myself to throw away rolls of crappy images that I know will never see the light of an enlarger. They get contact printed, numbered, and filed just like the keepers.