Grand Theft Auto I guess. I really can't think of many games that have improved by going to 3D from an original 2D.

Mario = worse
Zelda = worse
Metroid = worse
Final Fantasy = worse (couldn't get much worse, but FFVII accomplished that)
Mega Man = worse
Castlevania = worse
Contra = worse
Metal Gear = worse
etc.

 The bolded ones I agree with, but you have to be joking about the rest.

Not joking at all.

Super Mario Bros. 3 > Super Mario 64

Zelda LTTP > Zelda OOT

Super Metroid > Metroid Prime

Final Fantasy > Final Fantasy VII

Metal Gear > Metal Gear Solid

Mario 64, Zelda OoT and GTA3 are my picks.

 Sorry.  I respect your opinion, but I think we're on totally different pages here.

To each his own, obviously.  I much prefer the precise control and challenge of the above 2D games as opposed to polygonal graphics, cutscenes and dumbing-down of the 3D ones.

Definitely MG to MGS and GTA, as well as FF. Sorry, but Mario's transition was horrid, the best Mario I've played in years is Super Paper Mario, which was VERY good, of course this is my opinion, I just didn't like em, and Metroid even less for that matter.

I would concur that Mario had the most significant jump.
I would seem to think that the greatest improvement of the franchise in going 3D would be Metal Gear because the NES versions sucked (Moreso Snake's Revenge). This could be paralelled by other small franchises like Hydlide and to a lesser extent Shadowgate. I would say Sonic if you were to go from Sonic 3 or Sonic CD to Adventure, however there was a Sonic 3D title intermittenly that wasn't so smooth. Gex saw improvement in my opinion. Fighters = blah/blech. I liked Mario Kart better on SNES. Pilot wings = honerable mention.

In conclusion: 1. Mario, 2. Starfox, 3. Metal Gear, 4. Castlevania, and 5. Pilotwings

It seems to me the choice would have to be either Mario, Zelda, Grand Theft Auto or Metal Gear. All other series built off of what those four did. Other than the big 4th gen to 5th gen 3D switchover, GTA is the only one that did anything revolutionary with the jump. I mean, as much as I love the Metroid Prime series, they only really added a twist on FPS mechanics, which were of course both revolutionary (and pretty much inaugurated the move to 3D) and primarily developed via new IPs. Though I guess you could say Wolfenstein 3D deserves to be on the above list, if it wasn't for the fact that it doesn't hold up anywhere near the way the above mentioned four do.

For my money it would be Zelda. Ocarina of Time was the first game that felt to me to capture something of a vast open world--a world that felt real, as opposed to the finite boundaries of Mario 64's levels, or the endless unchanging and semi-uninteresting corridors of the first wave of FPS's.

Edit: Duh, none of this counts fighters, I realize. My answer would be the same, but obviously 3D fighters don't owe anything to the other mentioned games. Of course, that change was via an original IP as well.

Final Fantasy's was pretty good. Mario and Zelda are definitely in the top 5 or top 3 though.

I think a better question is what game series had THE WORST jump. In my mind it is still the Castlevania series. I did enjoy Lament of Innocence though.