I like having mine separated and organized. IJ, STTNG and TZ are grouped on one wall, AFM and MM together on another wall, POTC with LOTR on a separate wall and GB in its own corner. Very logical, but the truth of it is that my average guest would have no idea that there is a system to it at all, but it satisfies my sense of OCD!
MK6PIN: (Looks like you're fairly close to me, have to let me know if you'd be interested in joining a few of us in the area with about the same size collections to play sometime.)