I'm gonna enjoy posting this.
EarthBound: Smiles and Tears
Perfect ending song to a game with great music.
Mother 3: Master Pokey's Theme
This guy was a pain to defeat.
Mega Man 10: Wily Machine
The perfect music to the 2nd to the (possibly) last battle (ever) with Dr. Wily. Since Inafune left Capcom, I don't think there will be another Mega Man game. MM10's ending does seem appropriate for the story line to shift to the story of Mega Man X.
Alien Hominid: Area 51 (Map 3)
I only played the GBA version, and this was the only theme that it had for Area 51, I liked how it sounded, and this game was pretty good.
Super Meat Boy: The Rapture (Dark World [PC])
This was the Dark World theme they had for the PC version of Super Meat Boy. I always wanted to play this game, and listening to the soundtrack just made me want it more. This song just gets you pumped for the Dark World of the 3rd to the last Chapter.