For me it has to be Toki. The characters were so weird and creepy, especially the bosses!
Probably Morrowind. The game is ugly and the mechanics are a bit clumsy, but damn did I love it. Prolly clocked over 3,000 hours in Vvardenfell man.
I love Morrowind so much that I refuse to admit to its ugliness. I will choose to believe that the less-than-perfect graphics simply enhance the alien look and feel.
Same with the fog to cover up draw distance issues.
“It’s called an art direction sweetie, look it up.” But without any sarcasm.
The game mods that increase the view distance take something away from the games magic, IMO. To this day I remember walking down the road and seeing Vivec city suddenly appearing in front of me from the fog.
I think because I played so long ago, that for that time it looked to me fantastic.
I assume we are only talking about games that looked ugly pretty much upon release, and not games that look really bad now but are still really fun.
In that case starting with the most recent:
Save Room - Puzzle game that is just the inventory management from survival horrors like Resident Evil. Might be just a simple joke game, but I had a lot of fun with it.
Outcast - The voxel tech just wasn’t ready. Amazing game, one of the best of the era, but it its visuals left a lot to be desired. Modern updates have greatly improved its look.
Eradicator - This one was looking out of date when it came out, but its a surprisingly awesome and deep 90’s era shooter.
Kenshi. It’s simultaneously janky and beautiful.