Played Cave Story 3D in actual 3D recently, from all the shit I've heard on it, I was expecting a less then stellar 3D, in the end, it works pretty well, the 3D feels pretty good coming from beginning 3DS with no help from Nintendo at all.
The 3D doesn't really fix the issue that you have a hard time seeing characters but it helps still, I just remember a part in the egg corridor where I couldn't see a critter due to how blue it was though.