I'd have to say DQVIII or Ninja Gaiden. When Ninja Gaiden came out for the Xbox I shat myself it was so good.  

I mean, mario and zelda are pretty good too, ha ha

I still haven't had a chance to play the 3D Ninja Gaiden's unfortunately...

WHAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA????  You'd love it man!

I know. I just didn't have an Xbox, and when I had an Xbox 360 I didn't really know too much about it.

Metroid. Because it's more impressive to me than Mario/Zelda, since it wasn't as obvious how to make that transition as it might have been with the others listed. Plus, Retro Studios is located in Austin, TEXAS, and therefore is better than everyone else. 

I will say GTA was probably the biggest positive leap in quality from 2D to 3D ...

Before Retro Studios, there was Iguana Studios, who were famous for making some of the earlier Turok games.  I went to college in Austin at that time, and one of the things I did as a school assignment was interview someone at Iguana (I think it was David Dienstbier).  One of the things he said was that his team was working on a secret project.  I really think that secret project was Metroid Prime.

Sweet. I didn't like the Turok they released on GameCube, but I always thought the N64 games had a really cool concept. Only really saw a friend play one like once though.

Turok and Turok 2 are on Steam now. They've upped the draw distance and improved the controls dramatically, and they both run pretty well.

I honestly came in really late to a lot of these series and played them once they had transitioned to 3D. One of the series I didnt was Donkey Kong. I actually liked Donkey Kong 64. It gets a lot of hate from people but I enjoyed playing it. 

 This is why I disagree with you :p

Blake, did you just say you do not like DK Rap? That's immature of you. Have some respect.

Omg.....Im dying over here LOL! 

You two are crazy

The Nintendo titles on your list: Mario 64, Zelda, Metroid Prime, and DK64 were big for me.

I can tell you a series that did not translate as well in 3-D and that was Mega Man X.  MMX7 was awful in 3-D.  Although I did like the Mega Man Legends games, I don't think they've aged very well either.

I've only seen gameplay footage, and it looks all kinds of jank.

 Legends really doesn't feel like a Mega Man game though, despite being the superior of the two. I'd argue the series really hasn't translated to 3D well at all really. It's a shame, because a good 3D mega man game would be pretty fun.

Ratchet & Clank is what a good 3-D Mega Man game should've been like.

I can only think of how I hated those Duke Nukem games after DN 3D where it went third-person in immitation of Tomb Raider. Well, Time to Kill wasn't too bad. 

Mario 64. Yep, that's it. Completely blown away by the concept and the levels.

I don't think a lot of it holds up today due to the controls, but I will say I think Mario feels the best he's felt in 3D mario games. Later games made him a bit floatier, which is fine, but I think 64 feels better.

I'd probably go with Metroid Prime. It felt the most faithful while still creating its own experience. Most of the others were either superficial changes (FFVII, DQVIII) or changed so much it was a different game (Mario 64, Ninja Gaiden). Prime was a perfect middle ground.

That's a pretty fair reason. 3D Mario and 2D Mario almost feel like different series, while Metroid still feels like Metroid.

Metroid Prime! That visor had some cool effects!

Darn tootin.

For me it has to be GTA. I never got into the top down GTA stuff, but then came Vice City (I skipped over III) and then I was hooked.