Dark Sun, original Boxed set (because it was built as a baseline, and it expected GMs to add and interpret the material in their own way, whereas the expansions set too much in stone).
Jakandor gets second place, because it was just a COOL SETTING.  Native/Viking cross Barbarians fighting Aztec-like Wizards that have zombie and skeleton pets, in a fairly low-magic (for D&D) jungle setting, amidst cyclopean ruins?  I mean, you can't get much cooler than that.  Really.
Council of Wyrms gets my third vote, because it was a neat idea, and a neat setting.  The idea of playing a dragon, and then also playing in games as your dragon's mortal familiar is kind of cool, and any game that  really incorporates the passing of time as a necessity is cool in my book.  Plus, the few times I played Council of Wyrms, I got to be a Silver Dragon named Freddy Mercury.  And that's just AWESOME.  (Plus, the CharGen rules basically had "feats" that let you learn certain dragon attacks, rather than just learning them automatically - a sort of precursor to 3e's feats, in a way.  Kind of neat).