Basically the real 3D thing works by showing a polarised image alternating between the eyes, one frame for left eye quickly followed by one frame for right and so on which is filtered by the glasses and creates the 3D illusion.
All they have to do to an old film, is render each frame with this polarising technique, (I assume in a similar way to how they remaster old films to improve the quality) to make them appear 3D.
I saw The Nightmare before Christmas ...er.... before Christmas last year and it looked pretty good, to be honest though, in comparison to a film that was intended to be 3D with specific jump out of the screen effects like Journey to the Center of the Earth, it is nowhere near as good.