The new 3d is actually two pictures seen milliseconds apart. You wear glasses that plug into the usb port and the computer blanks the right eye and shows the left picture, then it blanks the left eye and shows the right picture.
They actually film with dual cameras. Your brain interpets it as your eyes do in the real world. If and when it becoms mainstream everything will have 3d even the commercials between shows. It's just a matter of " will this technology take off"
Currently the Tv and glasses are expensive and there are only a few movies out so people are not rushing out to buy the TV's and glasses right now.
To awnser your question, they will play the current standard videos as they look now. you will have to purchase 3d versions as they come out.