Preliminary note: I wanted to add a comment to the chosen answer, but couldn't add a comment, so I add it as an answer - I'm happy if anybody can move it to the comments.
I have tried the auto-align feature of
hugin (via the
align_image_stack command). I used it for a time-lapse sequence and it does not work well (probably, because there is too much movement of objects in the scene). Understandably,
hugin doesn't seem to be able to set control points only in the background. - So be careful with hugin for a full-automated solution.
Update: I now have tried the alignment feature in Photoshop CS5 with the same time-lapse sequence. The result is definitively much better via
align_image_stack. So, if you have access to Photoshop, give it a shot - it's worth it!