I'll try to keep this up-to-date as I find more sites. Feel free to comment and add more.
VGMusic - really well-done imitation of some warez sites that were closed down.
Homestar Runner - Nobody! Nobody! It's the King of Town!
Penny Arcade and PvP switched artists.
Fark - Farked by guinea pigs!
Something Awful - HOT BORING FETISH ACTION!
Lizard - Lizard goes all explodey.
Real Life - Dean's doing horribly in the humor department, but here's some sort of "what's the difference" strip.