It depends for me, I can play games easily with the 3D on about half. This excludes of course Rayman 3D which personally for me has some reaaaal issues with the way the 3D was implemented. I can play all AR games, and Monkey Ball 3D easily for hours without feeling any negitiave affects. Then I played Rayman 3D for 15 minutes got a killer headache and had to take a nap :/ not sure why this happens but Rayman for me at least has a lot of ghosting and depth issues.
For everything else it looks great and doesnt affect me at all, if you're looking to get OoT you won't be disappointed. I got to test the game back in Feburary through my work and it looked amazing, the 3D was very comfortable and smooth, no ghosting or depth issues for me.
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