Interpol's "Stella Was a Diver And She Was Always Down" on French radio is even better than the album version.
Glassjaw's accoustic "rehearsal" version of "Midwestern Stylings" blows the regular one away. Their second take of Convectuoso kicks the original's ass also.
I've always liked Blink-182's "Girl Next Door" better than Screeching Weasel's.
Deftones' live cover of Weezer's "Say It Ain't So" absolutely owns the original.
Oh, and Goldfinger's "Woodchuck"