The all-time number one would probably be The Principalities of Glantri, just for the sheer amount of use it's seen over the years. I got it at a time when I was only playing the boxed sets (never really did 1st ed AD&D), and it immediately sold me on Mystara. I've done three long term campaigns in the setting.
Other strong contenders:
Delta Green Countdown- already been mentioned.
Dark Champions- I don't even play Hero or Champions, but the original version of this book was probably the best street crime resource ever done. Haven't seen the new version.
Sharn- I'd always liked urban fantasy, but it was woefully unsupported until this came out.
Kult, 2nd ed (white cover)- 1st ed Kult felt too much like it was riding on the coattails of WoD, even if it was written largely outside of that game's influence. 2nd edition really amped up the disturbing weirdness and helped set the game apart.
Unknown Armies- I love Tim Powers, and this is as close as a game is going to get. I think modern occult magic should go along these lines- you can get the power, but you have to be willing to pay the cost. Also, the madness meter works much better than Cthulhu's sanity system, which is essentially just another version of hit points.
Castle Amber- Favorite module of all time. It's so utterly and bizarrely over the top that it could be renamed "Fear and Loathing in D&D". Also, much of it formed the basis for Glantri later down the road.
