Most of the 3e adventures I've really liked are from Dungeon Magazine. In no particular order...
Age of Worms: The Whispering Cairn - It might be brutally deadly for some first level parties (hint - encourage burning hands and flasks of alchemist's fire), but no module I've ever seen has so successfully combined 1e hard dungeon crawling with the emphasis on story and roleplaying 3e tries hard to encourage. Of course, I also loved the rest of the Age of Worms, so...
Steel Shadows - I'm a sucker for murder mysteries. I'm a sucker for warforged. A murder mystery featuring warforged? I'm sold. The clues are well set up, the antagonists are both wicked and surprising, and the fights are memorable and brutal. And yes, of course, this is an Eberron adventure, so it wouldn't fit into all games.
The Styes - More urban mysteries, this time with a heavy Lovecraftian flair and more than a little homage to the dark fantasy of China Meiville. And it was the first time I ever got a handle on how to use an aboleth effectively.
Shadows of Istivin - I haven't ran through it yet, but this three-part adventure arc is chock full of classic Greyhawk flavor. And it's got giants, drow and demons in it! A triple threat that's hard to miss with.
Demiurge out.