For stop motion animation, you are most likely going to need a remote shutter release. This will allow you trip the shutter, change your animation and trip the shutter again without touching the camera. A intervalometer is a timed shutter release system which allows you to trip the shutter over a predetermined time for example 5 shots per minute. I cannot see this as being very useful for stop-motion and is more a tool for time-lapse photography. A system that couples to a laptop as mentioned above would be ideal and if i remember that is what they used in corpsebride. this will allow you view the shot in your laptop with out disturbing your animation. Once you have taken your sequence then open it up in Quicktime pro as a image sequence and export to your particular format. Since most formats are now 16:9 native then it might useful to remember to frame for widescreen when your composing your shot.
Hope this helps