In no particular order...
Godlike: Superhero Roleplaying in a World on Fire 1936-1946 by Hobgoblynn Press
The best superhero RPG I have ever played. It eschews the most grievous clichés of the genre and interprets it in a realistic manner. The mechanics are quick and innovative, and the alternative history is the coolest ever. If they'd sent the X-Men to save Private Ryan, it would've looked like this.
Forgotten Realms Campaign Setting by Wizards of the Coast
This is a textbook example of how you make a setting book. 320 pages of dense text, and full-colour illustrations in hard covers, complete with a poster map. The setting retains the spirit and atmosphere of the old editions while updating it to the new system and strikes a good balance between setting material and rules items. It's well written, and there's an adventure hook or five on every page.
Paranoia XP by Mongoose Publishing
The Mongoose guys did what I didn't think was possible. They updated a dated product of the Cold War into the 21st century, while retaining the atmosphere and charm of the old editions. It seamlessly ties the old jokes with the new ones. Humour is a very difficult genre to work with, especially in RPGs, but Mongoose did it.
Call of Cthulhu D20 by Wizards of the Coast
I far prefer this version of the classic over Chaosium's edition. Production values are WotC's usual fare, and the rules adapt D20 system very competently to handle low-powered horror gaming instead of dungeon crawling. The book offers a great deal to game masters and players alike and is also a very good source for stuff to use in a D&D campaign.
Demihuman Deities by TSR Inc
A prime example of how to make a sourcebook about deities. I still use this and its companion volumes, Faiths & Avatars and Powers & Pantheons, frequently. Densely packed text that tells both about the deity in question and far more importantly, about the deity's church and the roles it plays in the world, which is what people are really interested in.
Honourable Mentions go to...
Uncaged: Faces of Sigil by TSR. If I actually owned this book, it'd have replaced CoCD20 on the list above. This is how you make an NPC sourcebook.
Dragon Magic by WotC. A very good accessory that is generic and very flexible in its use while still focusing on a specific theme and supporting a wide range of other products. A lot of good content in here.
I6 Ravenloft by TSR, as well as its later incarnations House of Strahd, Robinloft and Expedition to Castle Ravenloft. A most excellent adventure. It can be cheesy as all hell the way it plays off horror clichés, but Strahd is a truly terrifying and memorable villain when played right.