I would nominate the end of Sonic 3 & Knuckles for basically being the best possible way to end the quadrillogy. It's pretty much one of the most epic (in the old sense of a term) endings to any game series I've seen, for a variety of reasons I'll wait on explaining for now.
But, to be less obvious, there's Namco's The Outfoxies
. The whole game is sort of a proto Smash Brothers, mixed in with a bit of Rolling Thunder and Elevator Action Returns. You play as an assassin trying to kill a bunch of other assassins on places like a flooding aquarium and atop a train, so that this guy named Mr. Acme will pay you. There's no way this will backfire on you, right? (Spoilers: Yes, there is.) See 5:03.THE OUTFOXIES (BETTY DOE 2/2) game play
And so, your employers decide it'd be a great idea to piss off the assassin who's just killed six or so other assassins in mortal combat. It's a great setpiece that has some great music attached to it, and it's a great end for what's basically an interactive action movie. I think my favorite part is how much of an understatement "Betty Doe Won" is at the end.