I'm working on a 3DS RPG type thing in SmileBASIC. All the art and programming myself, and hopefully music if I make it that far.
If you can do the cross eye thing to see things in 3D, you can try it with this:
Pixel art with 3D off (still a Miiverse jpg though):
all the grass is blowing in the wind, normally it's straight. The little individual dark pixels scattered around are particle leaves that blow off the trees, and the clouds scroll up and to the right. The water also moves back and forth a little. Also not pictured is a Dragon Quest style swamp with bubbles that slowly rise out of it in 3D.
You basically have access to 5 3D layers, not including stuff that pops forward out of the 3DS which I'm not doing because it gets messed up at the edges of the screen. Water is on the lowest layer, then the ground and low things like trunks of trees, then a middle layer for trees and such, and then the uppermost layer for the tops of trees and tops of the mountains, finally with clouds one layer above that on level with the screen.