Anything Stevie Ray Vaughan covered is bound to be great. His version of Hendrix "3rd Stone From the Sun" on the El Mocombo DVD is amazing.
Frente's version of Bizarre Love Triangle (which I seem to hear at least once a week on the radio here in Taiwan - and I don't listen to radio at home).
Nick Cave "Black Betty" - it's hard to top the Leadbelly original, but Nick does a pretty good job.
Weezer "Hit Me One More Time" - at least I think that's what it's called - the big Britney Spears song that made her famous.
Any of the covers on Nirvana"s Unplugged CD.
Tori Amos "Smells Like Teen Spirit" - just piano and vocal.
Hendrix doing the Cream's "Sunshine of Your Love" - I actually read once that Clapton saw Hendrix for the first time, and got inspired to write a song. So he wrote "sunshine..". Hendrix then saw the Cream perform "sunshine" and was blown away, so he decided to do a cover. Don't know if that's true or not.
Joe Satriani - "Flight of the Bumblebee".
Velvet Revolver "Money" - a good version of the Pink Floyd song, and "It's So Easy" by Guns n Roses (although is it really a cover if most of the band are ex-GNR?).