The first stage of Ghosts ‘n Goblins for sure. (This Textile implementation doesn’t like links with apostrophes in it http://www.vgmusic.com/music/console/nintendo/nes/ghosts_n’goblins-_stage_1.mid )
All the music in Gradius is great but I love the first level’s the best (probably because I played it a million times).
Though I hadn’t played it much on the NES, I played the hell out of the arcade version of Bubble Bobble and whenever I hear the theme I’m instantly in a happier place.
They only had the title music to Commando which is nowhere near as good as the in-game or ending credits music so I won’t link to it.
For what its worth, MIDI sucks for these songs. Some people have made some really great chiptune renditions – I’ll try and find some links.