Alignment books - Book of Exalted Deeds and Vile Darkness are both very hit and miss. Some of the ideas presented therein are questionable (Look, Good is not just the direct opposite of EEEVIL!). Vow of Poverty will always be one of my favorite feats... there is a no religious / Exalted hangups version on GitP that I really like.
Complete Series - are very hit and miss. Complete Psi is the only one I do not intend to eventually collect. I have most of them already.
Draconomicon - A best in class WotC product. This book is beautiful.
Dragon Compendium vol 1 - a very underrated book. Battledancer is my go-to "Monk" (ok, no... thats Swordsage)
Eberron line - [MENTION=15800]Hellcow[/MENTION] gave us a pretty spiffy campaign setting.
Environment books - Frostburn is the only one I have in hardcopy so far, but I want the other two. I wish they had done more of these books.
Expanded Psionics Handbook - Despite the nay-sayers, Psionics is more balanced than Magic. Bruce Cordell has always been one of my favorite designers.
Fiend Folio, Monster Manual II and III - good stuff.
Fiendish Codex I&II - it is a shame that they never did FCIII for Daemons (yugoloths). Whenever my PCs get too uppity I throw Legion Devils at them...
Forgotten Realms Campaign Setting - no other book in my library has gotten as much consistant use since it came out as this one. The best CS WotC released. Best book of the FR Line.
Minis Handbook - half of the book is rubbish unless you play the Minis subgame, but this book gave us some cool Base Classes (Marshal, ok its good for a 1 level dip) and PrCs (War Hulk SMASH!)
Oriental Adventures - whats not to love?
Races of Eberron - the book that reversed my negative opinion of Eberron.
Spell Compendium - The resource for spellcasters.
ToB - Meleers can do cool things too?
Unearthed Arcana - a lot of good / interesting variants
Dishonorable mention: Book of Erotic Fantasy - because [MENTION=85158]Dandu[/MENTION] is a pervert.
3rd Party / Homebrew: The Tomes (
http://www.dandwiki.com/wiki/Tome_of_Necromancy_(3.5e_Sourcebook)),
http://www.dandwiki.com/wiki/Tome_of_Fiends_(3.5e_Sourcebook)),
http://dnd-wiki.org/wiki/Dungeonomicon_(3.5e_Sourcebook)),
http://www.dandwiki.com/wiki/Races_of_War_(3.5e_Sourcebook))) changed the way I think about D&D. Conduit of the Lower Planes is one of my top 5 favorite classes.