Top three, in no particular order:
Korn - Another Brick in the Wall
Puff Daddy - Every Breath You Take
Madonna - American Pie (this is the worst)
Whomever said Tori Amos' "Smells Like Teen Spirit" is one of the worst covers of all time, I guarantee you two things:
1 - That is a VERY good remake by ANYONE's standards. What more could you want from a cover? She did a great song in HER OWN WAY (hint Madonna, just doing the song the same way it was done before is a waste of your time and ours), and added something to it. When you hear Nirvana's version and her version, you're left with two VERY distinct feelings.
2 - I'm a HUGE Nirvana fan, and I feel like I have a pretty good grasp on what Kurt Cobain was like. He wasn't too proud to accept compliments, he just usually thought he didn't deserve them. I can tell you with 100% certainty that he wouldn't have had a problem with that song. A little creepy, very vocal, etc. He also clearly doesn't have a problem with covers since he did Meat Puppets covers for "Unplugged."