Warning, this list is heavy with the Michael Bay and Michael Mann love.
1) Heat, the robbery-turned-gunfight. The gold standard by which all movie shootouts have been judged since 1995.
2) Bad Boys, hangar finale. It was a tight race between this and the sequel's gunfight at the intersection (just before the chase across the MacArthur Causeway). I give the edge to this scene just because, well, you really can't go wrong with it.
3) Public Enemies, Little Bohemia. Between the Thompsons and Winstead's Winchester 1901, this probably wins for being one sweet-sounding shootout.
4) Transformers, USAF personnel vs. Skorponok. There are so many scenes in both this and Revenge of the Fallen that should have made the list. But like the earlier dilemma with Bad Boys I and II, I give the desert fight with Skorponok the nod because everything just comes together in this one. The AC-130 gunship helps, too.
5) The Rock, Marines ambush the SEALs. One of the finer moments in the movie, and probably that exact moment you realize that they're for real. The verbal exchange between Ed Harris and Michael Biehn is great, too.
Honorable mentions: Miami Vice (2006), final gunfight at the harbor. Shooter, the battle at the cabin. Die Hard 2...pick one. Die Hard, Karl and Hans corner McClane.