Rappan Athuk Reloaded: Almost probably the only Megadungeon published in the 3e era that doesn't suck (but this is my humble point of view).
Stonehell: In which Michael Curtis brings the One Page Dungeon concept to a completely new dimension.
The Castle Of The Mad Archmage: One of the best fun-made Megadungeons available for free.
The Caverns Of Thracia: Representing the early days of the hobby.
The Mines Of Khunmar: Even if an early draft, I consider Stefan Poag Khunmar The Megadungeon by definition. Probably the only published one in which I'd feel comfortable running a campaign in.
Under Xylarthen's Tower: I consider this awesome little (free) module from JRients to totally fit in the category. It's fairly big, with lot or room for expansion, and basically a small sandbox on its very own.
There are many other Megadungeons around I left out from this competition: Dwimmermount, ASE, Barrowmaze, Palace Of The Vampire Queen, The Black City, White Rock Castle, Ruins Of Undermountain, Greyhawk Ruins, etc. I decided not to let them in either because they still have to be published, or I don't really know them, or they're too difficult to pick and refer for comparison. Or I find they're total shit and they don't qualify for this competition.
Rules Of The Game
In each post I discuss one particular aspect of these dungeons: Presentation, Background, Keys, Maps, Level Connections, Usability and Creativity. Then I set up a poll and you vote your favorite the one that best represent said aspect. At the end of the competition, I compile a PDF with all the entries and poll results and declare the Absolute Winner Of The Megadungeon Arena.