Complete Book of Eldritch Might (Malhavoc)
Arcana Unearthed (Malhavoc)
These two are probably my most used - because I run an AU game, and I allow CBoEM spells in both that and my D&D game(s).
After that it gets murky, because even though I've got a fair amount of hardbacks, I don't use any of them nearly as much as I do the above. For sheer reading pleasure/inspiration, I'd give the nod to Beyond Countless Doorways, but I haven't actually used it yet...and Mutants and Masterminds probably doesn't count for D&D, so fill out the above with:
Monster's Handbook (FFG) - can't believe nobody's mentioned this yet
Freeport: City of Adventure (GR)
Unearthed Arcana (WOTC)
Now, if we get into softbacks, the choices are tougher. There's one that I have to mention though:
Book of Iron Might (Malhavoc) - best combat supplement ever. Even if you remove the middle two chapters. I am such a geek for this book that if I were to unleash the full amount of my geekhood everyone would run away and never read it, and Mike Mearls would probably go get a restraining order, so I try to tone it down.
For sheer 'joy of reading' Bastion Press gets the nod for both Airships and Alchemy and Herbalists. Both of these books keep asking me to change things in my game just so I can fit them in. Also good for inspiration are Malhavoc's Requiem for a God and When the Sky Falls - again, things that you might not want to just drop haphazardly into your campaign.
I think I'll stop the threadcreep before I get into PDFs...