Stickerbush Symphony has been one I'd like to hear, especially at a certain part before the percussion comes into the chorus part.
The K. Rool battle from DKC1 would be cool with more rock to it. Like how in One by Metallica, how it was all softish-medium until the end of the song. The guitar part of the song (the original) would be awesome.
I love the Brawl Squeak Squad Theme, they did a pretty good job. They had a great idea there.
I have been thinking recently that I'd like to see DragonForce, or at maybe just one of the gutarists attempt a tribute to Balloon Fight. Think about it. They start off with the main "dun dun dun dunn dunnn dunnnn daa, dun dun dunda, dun dun dun dunn dunnn dunnnn daa" then make some screeching noises like the flying enemies, then go into playing the Balloon Trip (main) theme.
I'll probably think of more later. Post your ideas.
Second Phase of Blizzeta. In rock or metal, it would be fantastic.
Nothing I can think of in terms of rock or metal. I've heard some very good electronic Mario theme remixes, though.
Wario World theme.
The boss battle theme from Final Fantasy Mystic Quest. Not a great game, but it had kickass music.