So, Mortal Kombat II Special by Hummer Team has the same music as Hummers' MK1 port, except for the character selection music. More specifically, it is based on the MK1 SNES port.
Mortal Kombat 3 Super Game music is based on the Sega Genesis MK3 port.
What's interesting is that some music tracks are so heavily rearranged that it is very difficult to find the original it's based on.
Here are the NSF files I've used. If some of you would like to help with my comparison, you should use these since I name the NES tracks by their number in an NSF file.
Mortal Kombat II Special:
http://www.mediafire.com/?aeaud1b7ijrzx0qMortal Kombat 3 Super Game
http://www.mediafire.com/?qlxkjsxa6c805i9Let's start with MKII Special.
Track 1 is obviously the Title tune from MK1:
http://www.youtube.com/watch?v=RLShhxspKvEminus the character selection music in the video
Track 2 is the character selection theme from MK2:
http://www.youtube.com/watch?v=UbW_tZOqqUcit is also the only MK2 track used
Track 3 is Battle Plan:
http://www.youtube.com/watch?v=0k6QVHg_m4ATrack 4 is High Score theme
http://www.youtube.com/watch?v=p6c4pRIgnJATrack 5 is Courtyard
http://www.youtube.com/watch?v=FoNBHUBpawITrack 6 is the first problem track. I could be either Warrior Shrine:
http://www.youtube.com/watch?v=Myj36cKcBQQor The Pit:
http://www.youtube.com/watch?v=lionPVq1-o8Track 7 is Ending Theme:
http://www.youtube.com/watch?v=vMRLak2KOQITrack 8: I have no clue what it's based on and need help
Track 9 is Palace Gates judging by the bass line in the latter:
http://www.youtube.com/watch?v=NCDu9r2lDFUTrack 10: I don't know really. It doesn't even sound like a MK music. Need help here.
Tracks 11. 12 and 13 are just jingles and are not interesting.
Let's check Mortal Kombat 3 Super Game/
Track 1 is Title Theme:
http://www.youtube.com/watch?v=uoBQhlmXCoYTrack 2 is a heavily rearranged Soul Chamber:
http://www.youtube.com/watch?v=FDQq9qxWJn8Track 3 is Character selection theme:
http://www.youtube.com/watch?v=UeIOnaCwpSQTrack 4 is some jingle I have no clue about.
Track 5 is The Subway:
http://www.youtube.com/watch?v=4KtEzIetww8Track 6 is Shao Kahn Tower:
http://www.youtube.com/watch?v=85tR6The4I8Track 7 is Pit 3:
http://www.youtube.com/watch?v=lnIlJAAhNjETrack 8 is my favorite in the game and is a real mystery. It has some feel of Soul Chamber, and could be yet another version of it, but the tune is too different.
Track 9 is also a mystery but it doesn't sound like MK music at all. Also I don't know where does it play in the game.
So that's all, any additions and corrections will be appreciated. Help me if you can guys