Super Metroid (SNES) - The boss in the space ship (Phantoon?), has one eye, along with the flames it shoots out. If that won't work, there's also the one-eye alarm thingy that alerts the space pirates when you get the Morph Ball.

The Sims (PC) - If you get the Livin' Large expansion, you can get a robot with one eye. He's an NPC, so it counts.

Link's Awakening (GB) - The Nightmare had one eye.

Majora's Mask (N64) - That eye boss from Zelda 3 appears again. This one's a tad more questionable since the objects surrounding it are clearly eyes, but those eyes can be knocked off, so they're more of a dependent species than an extension of the creature's body.