Back if anyone remembers, the fan game project by Arne, Megaman 21XX, used King of Fighters track Esaka 98' version I believe for the factory stage tune. I found a lot of King of Fighters music would fit in the X series well I believe. Same with some select Project Justice tracks, though that being another Capcom game doesn't surprise me much.
The snow resort stage for Gem Fighters, again Capcom, I think would fit really well in a classic title for a snow stage.
There was another from a game, I think was called Triad? I think the track was named Rolling Thunder, but I'm not sure. I found it on VGMusic once years and years ago I think. It sounded like it would work for a great 'first of the final stages'. Perhaps a sunset approach into the fortress.
I know there are more, but it's been a while. Perhaps I'll remember in time.