This is a set of instructions you can use to make stop motion animation with the Raspberry Pi. It draws really heavily from the wonderful Raspberry Pi Worksheet. I added a portion at the end that describes how you can get the images off of the Raspberry Pi using WinSCP and how to turn them into a movie using Movie Maker.
This is a wonderful project. If you have the Pi Camera, this is a great way to use it for making stop motion movies. It is a good introduction to the GPIO pins, and a great way to take pictures rapidly and manually. If you have any comments or thoughts, please let me know. I would be happy to make updates!