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.