If somebody every were to bend my arm to run 3.5e again, I'd run Rappan Athuk Reloaded straight up with all of the wilderness and side treks and everything. I've used Rappan Athuk as part of a campaign where the player-characters "raided" it for a special artifact. They went, almost had a TPK, found the artifact and got right back out. But they'd found quite a bit of other treasure, and wanted to go back for more.
In another campaign, a group of high level characters sacked the Upper Temple of Orcus. About a quarter of the group died, the rest were so weakened that they ran away from the mere spectres from a nearby room. (This is also where I learned that high level games in 3.5e can slow to a crawl).
In my opinion, there's two dungeons that if players have some success in navigating, they've got bragging rights:
The Tomb of Horrors