This is not the first time this has come up on the forums. I know, because I started a discussion thread on this soon after launch, which died a few weeks ago. :-)
With that said, I've got 5 3ds games so far: Pilotwings, Steel Diver, SSF4, Dead or Alive, and Ridge Racer. I have perfect eyesight, and I see the 3D perfectly. It is truly beautiful. Surprisingly, I think Steel Diver's 3D effects look best. Pilotwings I had to turn down the 3d to half, though after effectively beating it in 20 hours, I think it may have to do with constantly changing the focus of my eyes between the background/horizon and my flying vehicle. I also noticed that in SSF4, whenever Zangief does a spinning piledriver on my (Ryu), during the end of that when he's got Ryu ass up with his legs splayed out and one foot trying to stick out of the screen, that makes my eyes a little uncomfortable. Ridge Racer and Dead or Alive look great. No, make that awesome. They look awesome.