The poll asks me what the most common position is, so the answer has to be off, even though I like to use the 3D fully on a lot. The thing is, there's no real reason to keep it on unless ingame and I'm not always playing.
It also depends on the game. Usually, Nintendo games have a smooth 3D effect, one that doesn't bother you when you move your hands a little and that doesn't tire you out and well... in short bring the 3D to life. Games such as SM3DL, Kirby Triple Deluxe, Paper Mario SS, and so on and so forth. An example of a 3rd party game that feels as smooth as a Nintendo game to me is Bravely Default. In my head all 3rd party games have an obvious disadvantage to Nintendo games on the 3DS because obviously they know their hardware.
Another example is RE: The mercenaries. There's nothing wrong with its 3D, it looks good and gives you a good sense of depth, but since it's so intense, it's hard to keep up with the 3D, so I keep it off for this game. Same goes for RE: Revelations. My 3DS is the vanilla one, btw.