Probably 'Endlessly', first off. Every review of the album said that it was a weak track, but it's one of my personal favourites, as it's so beautiful and heartfelt.
'Fury', obviously, but that's a well loved track, only here because it should have found a place on our version of the album.
'Host' is a good track to listen to when you've just been dumped ( :'( ) so buying the Cave single was well worth it, and not a lot of the Muse fans I know seem to have heard of it, which is a tragedy.
Other than that, probably 'Eternally Missed', which is an amazing live track, and the music box type effect used is really strange, but fits that song well.