Don't forget about this:
http://www.youtube.com/watch?v=Jd3-eiid-Uw
That gets 3D with a movement illusion. With an accelormeter you could probably get a similar effect.
The other theory is that each screen has 2 screens, one for the left eye and one for the right eye which can produce a simlar 3D effect to the glasses in movies.
Not every game will have to take advantage of it anyway, if it's DS compatible then 2D games will have to be possible too.