just beat Zelda ss. besides some shitty programming with regards to onscreen text and hand holding, I really enjoyed it. as far as rendering/depth it worked perfect for me. the cutscene introing the last boss is just sublime in 3D, damn! overall in 3D - only issue I got was some minor shadowing with far away things but I think that might be attributed to my gen 1 glasses.
here are my settings when playing in either 2 or 3D (actually I cant play in 2D anymore):
https://skydrive.live.com/redir?resid=80C7DCC9A572A073!1120&authkey=!APEwpZ8-SDaBLG8
I also use sweetfx with default settings.
note: I don't enable 3D vision in the dolphin program as it crashes when you end your session. my computer automatically runs it in 3D so not sure why they even put that there. also, rendering at a res above 1080p doesn't work in 3D - I think it may have to do with my monitor. you will have to play with the depth and conversion in game to find your sweet spot. I imagine you know how to do this with the NVidia shortcuts.
and as a bonus here are some wind waker 3D grabs:
http://photos.3dvisionlive.com/eddiifox/album/50d2a5b7a3e0676c66000002/
fucking phenomenal!