My d20 shelf goes something like this...
Core books all the way on the right (but not the MM)
DM's reference material (BoVD, etc.)
Splat books from various publishers
Forgotten Realms books
Books of Eldritch Might I & II
DM screens and my folder full of maps
Many monster books from various publishers
Relics & Rituals I & II all the way on the left
The shelf above that one holds all of my modules and less-used material (like Scarred Lands region books, Greyhawk Gazetteer, etc.). Dragons and Dungeons sit in two large stacks on the very top of the shelf.
The majority of my non-3e gaming books are in storage, including most of my 2e stuff. I do have my FR and SJ boxed sets, FR regional supplements and SJ supplements here - the boxes sit on top of some of the other books, and the supplements are mixed in with the less-used material.
I definitely like it when my gaming shelves present a nice unified front (hardcovers next to each other, etc.), but the diversity of the d20 material is actually kind of appealing. Not the most logical layout, but it works for me.
Edit: Forgot about my 2e stuff.
