Sticking just to the NES for a second - the best music on the console early on was arguably never from Nintendo. Koji Kondo is a huge talent, obviously, but Nintendo was really pushing game size while other companies were bringing over arcade influenced experiences that pushed eye catching graphics and music.
So, I'm gonna go out and say Metroid was the most interesting. What Hip Tanaka did with that game was experimental art. I know Dread gets a lot of flack for not having a hummable score, but that's exactly what Tanaka was trying to do.
The middle two sections on the title theme start to give way to a melody, but the opening and closing sections are just oppressive atmosphere. There isn't anything above the ostinato! The sheer balls...