For me, the best D&D book I own is the Shackled City Adventure Path by Paizo (3.5E). It's my best D&D book because with it I ran a campaign for over 3 years and about 100 sessions, starting at 1st level and ending at about 18th-19th level. It was the longest campaign I've ever DM'd and the only one that reached the end point I'd hoped for at the start of the campaign. Yeah, I changed and added many things in the adventure (including a full re-write of the final adventure), but I definitely couldn't have come up with a campaign half as cool by myself.
Normally I'm complete bibliophile with my books. I hate to write in them at all or get them damaged. Almost all my RPG books are in pristine condition. By the end of the campaign, my SCAP hardcover was completely trashed. The front and back covers the book spine were all damaged. That wasn't because the book was poorly made. It was simply due to how much time the book spent in my bag as I took it to and from work to read on the train or on my lunch break. The book earned it's keep and then some.