Alignment of multiple images taken from the same point

If you are not making a panorama, but just aligning an image stack for focus stacking, exposure fusion or HDR, then align_image_stack from Hugin project is one of the simple yet very useful tools. Hugin is a multiplatform collection of tools that is available for Windows, Mac OS, and Linux.

For example, if your have 3 files a.jpg, b.jpg, c.jpg, to align them you may run:

align_image_stack -a aligned_ a.jpg b.jpg c.jpg

which will produce three TIFF images, aligned_0000.tif, aligned_0001.tif and aligned_0002.tif, which will be well aligned. Now the images are ready to be, for instance, enfused:

enfuse aligned_*.tif

If you prefer the graphical interface, or you want to align only partially overlapping images (like in panoramas), then use Hugin itself, it is a very powerful and flexible software.

Alignment of stereo pairs

From your comments I see, that you want to create stereoscopic images. The keyword to search for is anaglyph, not align.

For this purpose I used Stereo Photo Maker, which is not open source, just a free Windows program. It runs well under wine too. But I almost never used its automatic alignment feature, because I prefer to align images manually, watching the composite 3D image. By aligning the images manually I can also choose what exactly is “in focus” (one cannot align everything in a stereo image).

SPM can also optimize color anaglyphs to reduce ghosting, a very useful feature.

There are some scripts and tutorials for Gimp (e.g. anaglypher, script-fu-make-anaglyph, this short tutorial). It is relatively easy to build a monochrome anaglyph through layer effects and by moving a layer manually, it is not always working well for color anaglyphs.

Finally, there is -stereo option of composite command of ImageMagick, but I didn't use it.