Hard Drivin'... That game was so, so unbelievable in the arcades back then... mind-blowing stuff, really. Great game, too...
Oh, and I don't think I'd call late '90s stuff "early 3d model"... maybe, I guess, but still... I really wouldn't count, like, Outcast or Skies of Arcadia or stuff like that. "Early 3d" to me would mean at the newest N64, maybe, definitely nothing beyond that. Somewhere in the second half of the '90s is where I at least would draw the line, I think...
Dark Forces 2. Fucking awesome.
Best FPS ever. Yes, still.

1997 though, so it's not that "early", though compared to later stuff, or even some other games from that year, it does look somewhat primitive. The giant areas more than made up for that, though, not to mention the exceptional level design work, exploration, great music, puzzles, fun combat, force powers, multiplayer, and more...
Anyway, "early 3d"... Hard Drivin' is a fantastic one. As I said I remember being really, really impressed by that arcade machine. Mario 64 of course, to go a lot newer... that game pretty much defined "mind-blowing" for me. I still like N64 3d, really. Bad framerates, sure, but the better N64 games still look great to me... that's probably why I hesitate at including them -- "clumsy early 3d" to me sounds like "stuff that didn't quite work yet", but something like Mario 64 or Banjo-Kazooie... that worked, really well.
Something much more fitting would be, like, Vortex on the SNES... incredibly ambitious game for the platform, but unbelievably hard, and with a ridiculously low framerate and complex controls... despite how cool the idea is (transforming giant robot 3d flying/driving free-roam shooting game...), it just didn't quite work due to hardware limitations. Also, perhaps, Faceball 2000 on the Game Boy. 16-player handheld deathmatch in 1991!

(It isn't polygonal, but still.)