Some of my personal favorite enemies are the joy mutants from LISA. These guys hit a soft spot for me because of how creepy and weird they come off despite the cartoony art style. The thing that makes them stand out from other mutant type monsters, besides the art, is that they don't just add random limbs everywhere, or make them completely unrecognizable as human. Im not saying they're the best monsters in video game, just a personal favorite of mine.
Lincoln Nguyen
Guilty Gear Overture had some neat designs to it for its units, with each army having a unique aesthetic.
Joseph Baker
As shit as the game was, RE6 had my favorite enemies in the series Too bad the game was shit through and through
Jackson Murphy
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Colton Cooper
Binding of Isaac have some pretty cool looking enemies. My favorite is this hollow sack being airborne because of all the hundreds of flies inside him. Nevertheless in Rebirth I think the art style was a jab to much of the design, and the "pixelation" wasn't much better either. Not to piss on Rebirth at all, both games versions have their ups and downs
These dudes are especially nice in full context of meeting them. You would really expect many of the mutants' deformities to be a huge drawback, but instead they prove to be the toughest in all of the game. Not to mention the fucking music.
Brandon Martin
I like the angels in bayo. For two reasons.
One, flesh beings covered in cermaic and such are straight up cool. Two, this is a very pratical design in terms of gameplay because as you damage them more and more, the cermaic breaks off more and more revealing the flesh inside, thus giving you an immediate visual indicator of how close they are to death.
When your designs are both cool, and at the same time pratical and useful gameplay wise, you have mastered visual video game design as a whole and people studying how to make games should learn from you as a textbook example on how to get shit done propely.
Jace Jackson
I like what FF7 does with this one instance of taking an established fantasy creature and giving him modern clothes like he bought Parapa's old shit at Goodwill.
Evan Taylor
Kaneko's designs are god-tier (no pun intended).
Isaiah Cox
Doom engine enemies have always been fucking sweet as fuck. Dark, grim, yet not overboard. Same goes for Shadow Warrior and Blood.