3D mode is awesome (as long as you don't feel a little under the weather, it is not for those already-have-a-headache-gaming sessions.)
It looks very pretty and lively, and as has already been stated, if you go for a while with 3D, and then swithch it off, the differnce is really surprising.
Also: I've found the sinking lure in the fishing pond, I walked around a lot on the log where the big fish is. Young Link, mode.
A WEIRD WEIRD side effect is that I've started to dream about switching between 2D to 3D, it's like my sensory input has learnt a new way of experiencing things, so I dream of things switching from a stable flat surface to being layered in depths. (I dreamt of reading a newspaper, the photos, text and headlines got all layered and 3D-like when I switched in my dream) So I think being able to get used to having 3D available is a cool thing that might change some things in the way we percieve eye-input and sights. Truly odd.