I will omit all those wonderfull modern melodies from RPG games like
Final Fantasy, or action games like
MegaMan.
This is list of my favourite Nintendo Entertainment System songs: 
- Little Nemo - The Dream Master (1990) - Battle with The Nightmare King
- Ninja Gaiden/Ninja Ryukenden (1989) - Battle with Masked Devil
- Doki! Doki! Yuuenchi (1991) - The Final Battle
- Kick Master (1991) - The Final Battle
- Kage/Blue Shadow (1990) - Normal Boss Battle
Actually they aren't the best ones I've heard, but ones that I remembred first
That's because there were so many great songs, although some of them were quite repetitive
You can still feel the nostalgia
There is a link to the first song from the list -
Little Nemo Nightmare King's Dream OC ReMix - wonderfully arranged by
Shane Barber:
http://www.ocremix.org/remix/OCR01206/#
Enjoy!!!
Jam it back in, in the dark.
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My favourite NES Boss Music
lubik