I did something similar but I mostly used geometric shapes as enemies. (The game was programmed and ran on a 286) One of the bigger and more 'elaborate' enemies was an ellipse with eye-stalks and some tentacles (just wiggly lines, really). Imagine my surprise when many years later a similar creature spread across the internet. Somehow my enemy sprite of yore has an uncanny resemblance to the flying spaghetti monster that was invented much later.

Or wasn't it invented after all and I had a divine inspiration by the FSM, years before anyone else? Am I a FSM prophet?

hmm any modern pc game reference? All these old/console games examples have 0 connection to

I raise you the Great Mighty Poo.

Drakkhen famously had the dancing woman shadow. I remember thinking WTF first time I saw it in game back when.

Link: https://www.youtube.com/watch?v=cnE9XEC5mWw

Perhaps. Still, for all its faults Spore was a fount of entertainingly bad monster designs.
I'd mention some Shin Megami Tensei entries, but got to admit, even the worst monster from there was a work of art.
As for some stronger emphasis on the stupid, ugly, generic, and bad I'd nominate most enemies and bosses that debuted in Serious Sam 2, doubly odd because monsters from earlier games were pretty cool.
Think faithful recreations of characters featured in Nick Bouga's comics, for example.

There's a lot of latter day pokemon that I really don't think were worth the time of designing. And Jynx.

But why is that a wikialink when Bulbapedia is there?
It also had the laser panther, but that was radical.
Japanese culture has something of a (thankfully outmoded) fascination with that shit. Made localization anime a bit hard in the 90s, though.

Sometimes I feel a bit sorry for never having had to worry about such memory constraints when I learned programming :) I would've probably a great deal from it - that game was unfortunately horribly inefficient

Oh yes definitely, that's a religious experience if I've heard of one! If you could find that game again, then it could be the book, or rather code of revelation for the church of the FSM ;)

I have been thinking of buying Shin Megami Tensei IV on 3DS (a well known series that I have never played before), and it looks like the series has its fair share of bizarre monsters.