These two are my favorite musical moments in videogames.
The "Agro wanders the lands as you rest" idle scene is really cool to begin with, but to bury arguably the strongest musical track in the game in it is so ballsy-- and it just works perfectly.
And the opening credits to Final Fantasy VI. Something about the way it makes something beautiful out of such limited hardware always gets to me as well.
I generally don't think that videogame music is as good as other kinds of music, though, personally.