Looking at Ice Nine there's one example where 3D gaming was not horrible and not an eyesore. I really do get sick of people crapping on the 3D, because a handful of them did it well with a decent framerate, good control, and a nice story/whatever with it.
Wing Commander Prophecy stunned the hell out of me as it's all those levels of the PC game even some of the voice clips too, and the sfx intact...just missing the videos replaced with cutscenes. There's over 30 stages, decent challenge, plays quite well.
V-Rally 3 is the best of those 3D racers on the system and while the cars are sprite based, the entire terrain is molded and texturemapped in full 3D using a technique like the Saturn did in the day, and on GBA it's fluid, smooth, and no speed dips...has pop in but still a nice draw distance.
Mind you this one is a hybrid 3D/2D but GTA Advance is amazing. They remapped Liberty City from GTA3 in full 3D top down view (just like top view in the real game) and then moving objects(all) are well handled sprites. For the most part FPS stays solid, can dip occasionally but not an issue. Has a lot of cars, radio stations, sfx, music, all the rampages, taxi/cop/etc missions, standard story, the 100packages and more...it's nuts.
Max Payne on the GBA is amazing too...the entire game has the spoken dialogue of the PC game. Movable objects are all 3D based, areas are 2D isometic wannabe3D. Everything is quite hard, same stages, same bullettime and the rest...a real stunner they pulled off.
...and yah I saw DOOM1/2 get mentioned, they deserve it. Not so much DOOM1 as it's a Jaguar port, but DOOM2 is the full PC game entirely intact *except* one of the middle stages is so much larger than the others in the entire game they had to dice it into 2 stages...but they're still complete. Best DOOm2 on the go by far short of someones source code pet project on a flash card.
Fair enough to add that Duke Nukem Advance also is up there with DOOM, though the worlds are better crafted in a 3D area even with an up/down look mode, all the funny spoken duke-isms, and the rest. Compared to DOOM(either) it's short, but it's a great game with a lot of effects and stuff going on and it holds a steady framerate too.
That's about all I can think of on things I currently own that really jump out as a WOW...GBA did what? Impressive! type thing.