I store my negatives in Print-File archival sleeves (7 strips of 5 frames each, or 4 rows of 3 frames for 6x6 and 4 rows of 1 frame for 6x17). If I have more than 35 frames, I use two sheets, but I never squeeze two rolls of film onto a single sheet. Even if this wastes space, it makes things easier to find.
I file the negatives in chronological order: I write a serial number for the roll (4 digits for the year, plus three digits for the roll), and a brief description The sheets then go into Beseler plastic archival binder boxes.
Prior to cutting up the negatives, I scan the entire film strip using a Nikon Coolscan 5000ED with a SA-30 strip film adapter. The file names reference the roll number, e.g. frame 0 of roll 3 for 2008 would be 2008_003_00.tif. I back up the raw scans, then toss the scans of bad frames out, and import the remaining ones into Kavasoft Shoebox, my catalog program (eventually into Lightroom).
I use the digital files to retrieve the negatives as needed.
You could avoid scanning each frame (and the expense of a LS-5000/SA-30) by just making contact sheets and scanning them on a flatbed. I like having the scans for backup purposes, even if I hardly do any post-processing on them unless I actually need to print digitally or upload to a web server.