3D stands for 3 Dimensional. Real life is 3 Dimensional, meaning we are not flat. Animated movies are made in 2D. Meaning that they are flat or do not seem as though they are 3 Dimensional. It is possible to make a 3 Dimensional movie, but special glasses are required to watch it clearly.
Generally, in terms of 3D HDTVs or Disney Digital 3D, it means you have to wear special glasses to see a three dimensional image, instead of the traditional two dimensional image. The projector/TV displays the video at 120 or 240 frames per second, with 60 or 120 (respectively) frames meant for each eye (shifted slightly). The glasses allow each eye to only see the image meant for it. The result is that your brain perceives a three dimensional image.