Mother - the final battle. Giegue is possibly the only final boss I've ever felt a little bad for.
Earthbound - "Pokey Means Business" is some serious music. You go in, thinking it's going to be all awesome and fucking metal, and then he turns off the Devil's Machine. When you see SPOILER "the darkness absorbed Paula's call", it makes you wonder if you're doing it right.
Mother 3 - Events in the prologue and the final battle. I read somewhere that Itoi worked really hard to get the pacing of the lines in the final battle just right. I'd say it definitely worked.
The 7th Guest - You go through ALL THAT for an ending like THIS?