I know im in the minority here, but I did not feel the jump from 2d to 3d until the PS2. The N64 was god awful in that regard, it had a couple of games I absolutely love, but I dont really see them as "jump in graphics" or "jump in gen" games. Even OoT has so many drawbacks. And as asure as fuck It ruins Mario games for me. However, jumping from the fantastic FFVII, FFIX and whatever the fuck FFVIII was to decent FFX - to the fantastic FFXII felt important. Felt like a genuine change. So thats my pick.
Edit: And having that said - I thought - And still think - The SNES is the best console ever - To this day. So I cant really think of any "Jump of generation" that ever mattered as much.