With the exception of the Shackled City Adventure Path, this list ignores the many fine adventures seen in the pages of Dungeon magazine. While there are many that I thought were fine adventures, I'd definitely put in a word for the following:
Rana Mor (#86)
Glacier Season (#87)
The Seventh Arm (#88) Loved it!
Kambranex's Machinations (#91)
There was also a great drow-based adventure by Monte Cook, the title of which escapes me at the moment.
WotC: Return to the Temple of Elemental Evil
NG: Rapan Athuk (all)
WotC: Sunless Citadel
WotC:Forge of Fury
WotC:City of the Spider Queen
GR: Death in Freeport
PZ: The Shackled City Adventure Path
GR: Terror in Freeport
GR: Madness in Freeport
Return has a strong lead (and the ToE is doing well in both this poll and the 1st ed AD&D), with Rapan Athuk, Sunless Citadel and Forge of Fury all basically tied for 2nd place.
Crucible of Freya is tops in my book, packing enough information into a compact space to run adventures for MONTHS. WLD is great because I can piecemeal out the individual dungeons and plop them anywhere. Lost City of Barakus kicked ass because it could be placed anywhere and linked together with your own story for literally years of gaming fun.
The Gryphon's Legacy written by Wolfgang Baur published under the mysteriously vanished Gaslight Press is one awsome adventure if you can track it down. Sadly the empire building portion of the campaign vanished with Gaslight Press, but the adventure is top notch and makes a great base for new characters.