If you're sticking with physical media, I'm partial to the binder option. Compact, easy storage (toss on a bookshelf), easy access, reasonably safe if kept out of the sun, etc. No problem keeping things in order - simply use a spreadsheet to track disc location in the binder: book, page, position. No worries shuffling discs to maintain proper order, since the physical order doesn't matter. When browsing for music to listen to next, simply scan the spreadsheet rather than flipping through masses of physical discs.
At least, that's what I'd do in your situation. I've shifted to media-less listening, in part as a result of the challenges associated with the above model. (Now I use the same model as above for archival discs only.) It's awfully nice not dorking around with all the binders anytime I want to listen to something, now. Instead, I just pull it up in Foobar, on my Squeezebox, or on my iAudio M-3 (which of course doesn't hold -all- my music, but I don't feel the need to carry every single recording around on the train, etc.). I'm sooooo happy I stopped investing in audio storage solutions and made the switch to media-less listening. Just a thought.