Came in here about to post some Junya Nakano, but I see he's already been covered. Junko Tamiya has a few atonal pieces sprinkled throughout her soundtracks. It's hard to find links on youtube.
Strider - Introduction 1 & 2
Strider - Capture (
http://www.youtube.com/watch?v=XUMSR...RzUbH0I#t=155s)
Bionic Commando - Introduction Part B
A few tracks in Street Fighter 2010: The Final Fight
Streets of Rage III - Bad Ending (
http://www.youtube.com/watch?v=ikFFaieNr1o)
Streets of Rage III - Fateful Meeting (
http://www.youtube.com/watch?v=MH831upULq0)
Streets of Rage III - Kama de Coco (
http://www.youtube.com/watch?v=Cge_M7Iss5I)
And I guess most of Koshiro's SoRIII tracks in general, but mostly because of the experimental nature and use of automated sequencing
I don't know, would this be considered atonal?
Castlevania: Harmony Of Dissonance - Luminous Caverns (
http://www.youtube.com/watch?v=H-qHCZHDBh4) I have no idea what I would base the key off of. Perhaps the boss theme, too. (
http://www.youtube.com/watch?v=I-mOTc_O0aY)