Romulus: Awesome examples guys, and I thought of another: Sin.
I remember playing it when it came out and thinking that it looked a bit shoddy in places, but serious, it looks really awful now. The game was excellent, though hard as nails; I remember constantly having to reload saves almost every few minutes. I don't remember completing it without cheating at the end because it got so tough.
Have a look at the Gamespot screen shots and you'll see what I mean. That sniper rifle was so badly conceived, it looks like a damn scaffolding pole.
But besides all that, the characterisation was great, and story was cool too. When Emergence came out on Steam in all its glorious tits and ass, I was over the moon as the episodic content meant that there should have been loads to come. Alas, it was clearly never meant to be, as the developer got bought out. Epic sad face :-C

Antaniserse: System Shock 2:
yes, i loved every moment of the game, and the rendering of the environment/mechanical stuff is good enough, however all human models are absolutely awful, even compared to the low-poly standard of the time. (all the human models in Quake II engine based games, for instance, were by far better looking)
Even worse is how they look in the few pre-rendered cutscenes, including the ending one, what a letdown!
Heroes of Might & Magic 3:
I really liked both the gameplay and the art stile of chapter 2, and while HoMM 3 is a superior title in every aspect of the gameplay, the new graphical style, while on the surface more detailed, looked instead very confusing, grainy and dull.
Proof:

lowyhong: With all credit due, I'd still say Dwarf Fortress. Solid, addictive gameplay, but I honestly feel the game deserves more than just ASCII graphics. Even with the icon replacement packs, the graphics still don't do justice to the game.
Ah but what am I complaining about? Gameplay > graphics. Always. I can bitch forever about games with insane graficks, but then the gameplay... *ahembioshitahem*

lowyhong: With all credit due, I'd still say Dwarf Fortress. Solid, addictive gameplay, but I honestly feel the game deserves more than just ASCII graphics. Even with the icon replacement packs, the graphics still don't do justice to the game.
Ah but what am I complaining about? Gameplay > graphics. Always. I can bitch forever about games with insane graficks, but then the gameplay... *ahembioshitahem*

Horus: To me, Heroes II graphics are really good, but Heroes III are better.

captfitz: heroes 1 and 2 graphics had more charm, heroes 3 graphics were more polished.

Antaniserse: 'Polished' is not the term i would use myself, but i agree that it wasn't really "bad"; they tried to stick too much details in every sprite, and the result was a bit less functional to the gameplay

Antaniserse: The worst offender is, of course, Heroes 4, but i didn't mentioned it because it belongs to the 'Bad Game - Bad Graphic' category ;-)

sheepdragon: Haven't really played much of it to say anything about it, but Operation Flashpoint is probably the most ugly 3D game I've ever seen in my life.

chautemoc: http://drog.terra-arcanum.com/highres.html#screenshots ;)

cioran: Oh goodness. I didn't see that post. IMO, this wins easily. Great choice. Way better than mine. That game looked atrocious when it came out. Looks worse now. Pretty good game though, even if it had the usual Troika problems (buggy, broken quests, etc).