It's pretty much common knowledge by now that X-Men vs. Street Fighter pirate uses music directly from Street Fighter II, and that the Pokemon platformers use music from Bonkers. But there's another sound engine that seems to show up in pretty much every pirate that uses semi-original music.
Turns out that it, too, is from a Capcom game-- namely, Super Pang, a.k.a. Super Buster Bros.
This one's used in Pokemon Stadium, Tekken, and that Super Big 2 game that I saw on NicoVideo a while back. Pokemon Stadium and Super Big 2 both use a fanfare from Super Pang; it's track 28, "All Clear", in the music rip from SNESMusic.org. The sound effects are identical too.
And of course, the pirates actually apparently re-coded the Gravity Beetle theme from Mega Man X3 for the Super Pang sound engine; it's not ripped from MMX3 at all. Seriously, what.