I wrote a Skeinforge plugin that adds a new G-Code command, M240, to trigger a camera to take a photograph. This allows you to create time-lapse videos at one frame per layer of print. Two of the modes also allow for the location of the platform to be aligned between frames. One uses the minimum Y, minimum X corner of each layer as the photograph position and the other just tries to minimize the distance between subsequent layers.
You can see an example of the latter in this print:
http://www.youtube.com/watch?v=T3j5oXpqWCk
There is more information
on my blog.
