I may as well get this one out of the way, since Ladd got the other obvious one:
Rockman X3 - "Neon Tiger ~Urban Jungle~" vs. Guns N' Roses - "My Michelle"
It's worth noting that Kinuyo Yamashita (the musician for X3) has stated this is "purely a coincidence" as he'd never heard this song before he created this tune. I'm a bit skeptical, but I've had something similar happen to me, before, so... (My S3M for Slashman's theme is called "Jurassic Jungle" which, at the time, I didn't know was his boss intro message in Rockman 7. x:)