Release of tension. This is quite obvious. When the body becomes deeply relaxed in meditation, muscles start to relax. Usually this would be felt as twitches and small movements such as your thumb jumping, but it could also be a larger movement – your head might suddenly turn.
Increased flow of energy in the energy field moving through blocks. This is a more esoteric explanation, but you may actually feel the movement as being associated with “energy” (see some of the comments on the Sensing Energy during Meditation post). In this case, deep meditation is opening up some energy pathways and as more energy starts to flow it can hit up against blocks. As the energy dissolves the blocks, the body may spontaneously shake or twist and turn since everything that happens in our energy field is reflected in the body. (Read about the Human Energy Field.)
The question then is, what should I do about this? There’s really nothing you need to do unless the movements are too strong or disturbing you in some way. If that’s the case, you can simply open your eyes. This will help you to come out of the deep state you are in and the movements will naturally subside. Take it easy and come out of meditation slowly.
If the movements don’t disturb you, just let them happen without trying to manipulate them in any way. It’s better to not get involved with the movements, trying to make them happen or continue. Just let them happen spontaneously on their own, not resisting them and not getting involved with them. In a sense, you can treat them like thoughts in meditation.