"Zelda 3 - jellyfish boss in the 2nd Dark World dungeon has one eye (unless the satellite creatures count)"

I don't think it matters that it has satellite creatures, because they don't have eyes of their own. They just look like orange popcorn puffs.

Hyper Zone - In the Bio Plant level, if you hit those purple things, they open up a single big eye and zoom right at you.

The Simpsons: Bart vs. the Space Mutants - Many of the Space Mutants have only one eye.

Alpha Mission - One of the bosses is a green mechanical squid-like thing with a single eyeball.

Arcana - Cyclops enemies.

Samurai Shodown - Yagyu Jubei wears an eyepatch.

I Crawl and 1000
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And the tubes they glow in the dark
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And I'm here in Echo Park" - Warren Zevon