Mega Man 4 - One-eyed flying spiked enemies in Skull Man's stage. Also, those skeleton robots have a single red eye.

The Legend of Zelda: Ocarina of Time - The first boss is a one-eyed Gohma. I believe those one-eyed Tektites are also in this game.

Azure Dreams - The Cyclone familiar has only one eye.

Koudelka - I'm pretty sure there were several different enemies that had only one eye.

Kartia - Almost all Shadow phantoms have only one eye.

I Crawl and 1000
My site - Flying Omelette's Kitchen
My ezboard - Flying Omelette's Kitchen
MIDI of the Moment - Castlevania 2 - Bloody Tears
"I hear mariachi static on my radio
And the tubes they glow in the dark
And I'm there with you in Ensenada
And I'm here in Echo Park" - Warren Zevon