Aligning can be done for example with stitching-programs like Hugin.
- add all you pictures to the hugin-project
- let the pictures be analyzed/matched by "align image stack" (Images - Tab: Feature-Matching)
- add some points if needed (Control Points - Tab)
- set optimization to Position and Translation at the most (Optimiser-Tab)
- Optimize (Optimiser-Tab)
- check with "Preview panorama" (button above)
- go to Stitcher-Tab, set Projection to "Rectilinear"
- choose Output as "Remapped images"
- stitch! :D
You will get your pictures remapped into several exactly overlapping ones in the choosen format/size (Stitcher-Tab: Autocrop can remove nonoverlapping borders). It's a nice side-effect and prerequisite of stitching, I used it to create ghost-images (people swinging down a slope: put them five times into one picture), just stitching them together later (using enfuse/enblend on command line).
Hugin can do much more (like every decent stitcher, I guess), for example remove your barrel distortion and also vignetting. Look into optimizations for that.
hugin(via thealign_image_stackcommand). 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,hugindoesn'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 viaalign_image_stack. So, if you have access to Photoshop, give it a shot - it's – halloleo May 16 '13 at 06:38