Alright here's some I can think of. They might not be completely atonal/they may have tonal centres but they're generally chromatic and wtf-y anyway.
Alien Soldier~Blacksheep
http://www.youtube.com/watch?v=GOWmV2gcNzI
Alien Soldier~Lurk!!!
http://www.youtube.com/watch?v=bCeyxOUX4oE
probably other Alien Soldier as well.
Seiken Densetsu 3~Black Soup
http://www.youtube.com/watch?v=-0Vf4kVvE2Y
Super Bomberman 2~Bomber Battle
http://www.youtube.com/watch?v=Diliy2Lxbik
Jewel Master~Demon King
http://www.youtube.com/watch?v=rhY7Y058YTc
Shining Wisdom~Distorted Reality
http://www.youtube.com/watch?v=-k9j-N1t_i0
Secret of Mana~Danger (probably obvious!)
http://www.youtube.com/watch?v=v5FR_i-EbDc
Ogre Battle~Dark Matter
http://www.youtube.com/watch?v=i5m-9cm4UB8
E.V.O~Unnatural Threat
http://www.youtube.com/watch?v=iQZ8NgsOvgM
Granhistoria~The Machine
http://www.youtube.com/watch?v=iPwGrfq5wzk
Need moar boss themes like these. Dunno if they truly qualify as atonal but it's more or less my understanding of the term. See what you think.