OK, so you are looking for the way to get a high-quality stopmotion animation with your Linux? (by «high-quality» I mean that you want to get the image from your Canon/Nikon DSLR camera, not the cheap webcam or dvcam).
Meet the Entangle! An awesome tool for Tethered Camera Control & Capture.
And yes, within the recent versions they provide transparent overlay feature, which makes it suitable as a tool for the basic stopmotion animation.
I have tested it with Canon EOS 450D and it worked out-of-box for me, without any initial setup. Note, that for live overlay you need to have enable Live Preview in the camera itself first (in my case it is enabled by «set» button and available only when camera in P/Tv/Av or M mode).