For a librarian, I'm not very into "organizing" my D&D stuff. The limited number of potential users (one) and the relatively small size of the collection (a couple hundred books) and the fact I'm taking a lot of them out and using them and not putting them back makes it kinda pointless.
However, what organization I do have goes kinda like this:
Very inaccessible (boxed up, not even in my office): Old AD&D stuff I don't anticipate using any more, probably ever. Sad but true!
Somewhat inaccessable (on shelves in my office but not "handy"): Old AD&D stuff that I might very well refer to sometime in the next few years. Includes boxed sets (Dark Sun, Menzoberranzan, Birthright, Planescape). Also includes "pristine" copies of some works I've been published in (a couple of issues of Dragon) or otherwise want to preserve (a copy of "The Hermit" autographed by Gary Gygax). Also includes older handwritten notes from prior campaigns (before I started using a computer to do stuff).
Accessible but honestly not used much (on a handier shelf): The d20 Stuff I've kept (as opposed to the d20 Stuff I've given away to my players and at Chicago Game Days 1-3). Includes various hardcovers from FFG, some standalone game products, my Alternity books for some reason, other stuff like that. Also in this category are my old Dungeon magazines.
Very accessible (likely to be in a pile right next to my computer) are my core books and the books I'm using in my campaign (FR stuff, psionics book, campaign notes).
Currently under study (in a special location like "Next to Bed" or "Bathroom Library"): Works I'm currently reading or like to pick up and browse through when I'm just hanging out. Usually includes a couple of current issues of Dungeon or Dragon, and various D20 books that I think I might try to incorporate into the current campaign.
Electronic: PDFs, the SRD as saved web pages, and other doodads are on my computer in a special file, with a system all its own...