Hmmm, best by 'What I Liked the Best':
Book of the Righteous, really deserves a game world to go with it's great pantheon.
Hollowfaust: City of the Necromancers. A really fun idea. (Sword & Sorcery Studios)
Skull & Bones. What can I say I just like it. Then again, the 16th and 17th centuries are my favorite period for RPGs.(Green Ronin)
Monsternomicon, a monster book that exists both as a game tool and in the game world. (Privateer Press)
All the King's Men. I just loved reading this quirky, funny, yet very well written mystery adventure. Edge of Dreams by the same company is also very, very, good. Too bad they have stopped writing adventures. (Monkey God Enterprises.)
Best by 'What I Use the Most':
Seas of Blood. Very simple sea battle system. (Mongoose)
Sorcery & Steam. I just plain like steam age stuff! And I run Iron Kingdoms...

(Fantasy Flight)
Strongholds & Dynasties. Awesome. And it works with Seas of Blood. Makes me want to dust off Birthright again. (Mongoose)
Powerclass: Hedge Wizard. Cheap and useful, Hedge Wizards have pretty much replaced adepts in my games. (Mongoose)
Powerclass: Noble. Again great for NPCs.(Mongoose)
Common Grounds 2. Something to pull out when I am rushed.(As I too often am these past few months) (Bard's Productions)
'Most Used Pieces of a Larger Work':
Libraries in
Quintessential Wizard.(Mongoose)
Open Mass Combat System in
Quintessential Fighter (With the OMCS 2 in Strongholds & Dynasties this is likely to change.)(Mongoose)
Called Shots (I first encountered these rules in Swashbuckling Adventures, but I don't think they started there.) (AEG)
Best PDFs:
A Magical Medieval Society: Western Europe. Now available bound. This is a great book for setting up a more closely medieval campaign. And it has a test... (Expeditious Retreat Press )
Campaign Planner. Not much to look at, but very handy. (Ronin Arts)
Book of Templates. More, i WANT MORE! (Which is about the nicest thing you can say about a book like this...) (Silverthorne Games.
The Auld Grump, hmm, much of this appears to be by Mongoose...
*EDIT* And 'Most Likely to be Swiped from for My Own Stuff': The format used in the Creature Collections, the best laid out books in 2e were the Monstrous Compendiums, and this is as close as you can come in 3e.