I'd say A Link Between Worlds, the 3D effect looked great - not too strong from memory though - and really added depth (pun intended) to the dungeons.

Super Mario 3D Land was a close second for me. Having 3D enabled made platforming easier, and the 3D puzzles weren't the same without it.

Pokemon X/Y looked great in battle scenes, but loses points for having a 2D overworld.
Any other contenders?

P.S. Feel free to name and shame 3DS games with a horrible 3D effect; I'll start it off with Rayman 3D.

I love 3d in SSF4 for 3DS. Also like it in Fire Emblem, Etrian Odyssey and Bravely default: menu overlay look sweet in 3d.
Don't use it in Mario Kart - 3d effect is cool there, but during a race i often lose focus and its just hurts.
But best 3d - is in Zelda Link between worlds.

Aside from Link Between Worlds, I think I actually tend to get the most out of the 3D effect in eShop-only games. Ace Attorney looks fantastic in 3D, though it really adds nothing to the gameplay. Pushmo/Crashmo and Sakura Samurai come to mind as well.

Professor Layton and the Azran Legacy looks awesome in 3D. But yeah, that doesn't add anything to the gameplay either.

Spirit Camera, without a doubt.

I´d say:

Super Mario 3d World and A Link Between Worlds were the games that made the best use of it on gameplay.

But Pilotwings and Kid Icarus Uprising have the better effects, in my opinion.

Both Zeldas (OoT is too much on full 3D. Needs about 2/3 strength), Dead or Alive, Resident Evil Revelations (you'll have to go to the game settings and remove the restriction on the max 3C strength) and Mario Kart. For some reason, despite all I've heard, the 3D in Mario 3D Land was meh to me, yet everyone else seems to think its great

I loved the 3D in Fire Emblem

Just what I was about to write. 3D Land and ALBW made the game better and a little easier to play in 3D.

Pilotwings, a launch game, still has the coolest 3D effects though, many bad 3D games almost looks like they just push the whole screen an inch back, but in Pilotwings the player always is near the camera, while the background feels like it's really far away. Realistic too. I usually play Pilotwings with the 3D slider halfway up though, that's the sweet spot in that game for me.