The one that is coming out on dvd is in 2D only from what I have heard. I have heard that it is not coming out yet in 3D, but like mentioned before, if/when it does it will be the paper cardboard glasses, and not like the glasses, that you would have seen it in the movie theaters, that are not made out of paper.
Avatar will be released in 3-D as well as 2-D. Both versions will come in one DVD, and the option will be available on the menu screen. Paper glasses should come with the DVD as well.