Street Fighter 2010: ceiling eyeball
Abadox: weird eyes all over the place
Mega Man: one-eyed rock blob
Mega Man III; return of one-eyed rock blob
Zelda II: Moas
Castlevania II: floating eyeballs
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Street Fighter II: Sagat (only has one eyeball, because he lost an eye)
Street Fighter II Champion Edition
Street Fighter II Turbo
Super Street Fighter II
Super Street Fighter II Turbo
Street Fighter Alpha
Street Fighter Alpha 2
Street Fighter Alpha 3
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Adventure Island - one of the boss heads has one eye
Wonder Boy in Monster World - features the same boss head
Life Force: Level 1 brain with eye
Chrono Trigger: What was that boss skeleton's name? it had one eye. Dalton too.
King Arthur's World: features ogre bosses
Demon Sword: At the end, Viktar throws his completed coat-rack of death at a big eye.