It all depends on what you mean. If you mean retaining the spirit of the original gameplay while transmuting the medium to the third dimension, then I think Mario pretty much has that one nailed; all of the 3D entries play and feel like faithful 3D adaptations of a 2D system.

In terms of changing the gameplay best to suit it for 3D, I'd say that Metroid had the biggest task cut out for it, and did the most impressive job of remaking itself for a medium that it was never really intended for. Say what you like about Zelda being well-adapted, but it was a series that lent itself to 3D far more than a side-scrolling exploration-based game like Metroid.

For the improvement of visual style between the 2D and 3D spectrum, Dragon Quest definitely takes the crown (well, DQ8 onwards anyway; we'll forget that DQ7 is technically 3D). The realization of DQ artwork in 3D was no small task, and Level-5 did an amazing job of it.

As for the series least impacted by the transition, Final Fantasy comes to mind. It took until FFX for the games to even get full 3D environments (at which point they ended up losing detail in favor of being larger), and though the battles have been in 3D since FF7, they still all play out like their 2D counterparts, with the addition of spastic camera work to help induce nausea in more queasy players. I've nothing against the series, but I can't help but feel that Square-Enix has made the least impressive effort of all companies listed in this post thus far to really make the most of 3D over 2D.

What he meant was MGS was the game that initaiated the 3D jump. For once I agree with Leo-J on this.