Sonny is a flash game that has simply mind blowing music. Epic hardly begins to describe it. Just listen to the the battle music or the boss battle music and see for yourself.
Aftermath between fights, and Aftermath 2 for the second game. Just to name a few more.
To varying degrees, all eight tracks from the flash game, the Arrow of Time
The online Flash game series MARDEK RPG has some pretty sweet music, especially for the battles. You can listen to it on its website here.
Erasure's "Always (2009 Mix)", used as the background music to Robot Unicorn Attack, to absolutely wondrous effect. Warning: Ear Worm ahead.