Just a few notable omissions from the top of my head:
Earthbound - For all the hype, it really does have one of the coolest & most "open" game endings
Lunar: Eternal Blue - EPILOGUE. 'nuff said.
Metroid - It had multiple endings!
Chrono Trigger - Again with the multiple endings... lots and lots of them
Bionic Commando - You get to see Hitler's face "EXPLODE" in slow-mo
Super Mario 2 - It was all a WHAT?
Super Mario 3 - Come on... it's the princess and she makes a funny.
L.A. Noire - Character you like less and less throughout the game redeems himself, and you realize how your hard work and sacrifice really was, essentially, in vain. Still sort of stirs my ire.