I'd have to pass on Minish Cap going to 3D; the game has an art style and overall feel that seems "meant" for two dimensions rather than three. And, really, I felt overall pleased with TMC the way it is. I don't think transitioning it to 3D would make it any more enjoyable for me!
There are four games that I would love to see have a functioning Z-Axis among other 3D related things, though: Four Swords, Adventure of Link, Phantom Hourglass and Spirit Tracks.
Four Swords (GBA)
Okay, okay...I love FS. It's an amazing party game, or a game for just you and another member. But I can't help but feel that the game is arbitrarily limited by the 2D plane. Allowing the game to cross a dimension would do wonders for me, personally. It would free the thing up, possibly introducing new locales along with new ways to handle gameplay. :3
Adventure of Link
The mythical Black Sheep of the series, AoL is literally the hardest game in the Zelda series by general consensus. Partly because the AI is top tier, partly because the controls are a bit clunky...the game is just hard. But, another factor that plays in it is that the game is 2D, so you can essentially move left and right, or jump. I'm sure adding depth to AoL would ease the tension just a little bit.
Phantom Hourglass & Spirit Tracks
My biggest problem with PH and ST, aside from the touch controls, is that Link just cannot mantle any objects. It's ridiculous. The game really needs a third dimension to make it feel more like a Zelda and less like a separate IP in my opinion.