Align a stack of photos

There are occasions where it is necessary to align a set of otherwise identical pictures:

Aligning red, green and blue channels to correct chromatic aberration.
Aligning photos taken over a period of time to create a time-lapse movie.
Aligning bracketed shots to create a single HDR or contrast blended[*] image.
Aligning photos taken at different focus distances to merge into a single extended Depth of Field image.

Panorama tools is particularly useful for this process since it allows sub-pixel alignment and has a sophisticated lens correction model for applying distortion - Even photos taken years apart with different cameras can be aligned perfectly.

Most tools for HDR generation such as photomatix[*] have some level of automatic alignment, so this may be sufficient for most purposes. Otherwise the hdrprep perl script automates the process described below:

Aligning with hugin

Start up a new hugin project for each series and load the images. Set the Field of View, lens parameters and projection type, ie. if your lens is a fisheye, set this for both the input and output projection.
Create control points via the Photos tab. Align_image_stack is specialized for this task. But also Panomatic or Cpfind work for this use case.
Select "Positions (y,p,r)" and "Optimise now!" in the Photos tab.
If necessary, fine tune the control points in the Control Points tab and optimise again.
In the fast panorama preview, the images will be on top of each other. Select "Move/Drag" and "Fit", then select "Crop" and "HDR Autocrop".
In the Stitcher tab, select "Calculate Optimal Size", then deselect the default panorama outputs and select "No exposure correction, low dynamic range" in the "Remapped images" section. Select "Stitch!".

See a more detailed view of this article here.