The Hugin panorama stitcher can be used to align pictures. The align_image_stack executable is part of Hugin and can be run as a standalone command line program. To align pictures im1.tif im2.tif, im3.tif,..., you can give the command
align_image_stack -a al -C -t 0.3 -c 20 im1.tif im2.tif im2.tif ....
which will output the remapped aligned pictures al0000.tif, al0001.tif, al0002.tif, etc. Here the -a option sets the prefix of the remapped image files, chosen to be "al" in this example, -C means that the output files are all cropped to the same size, "-t 0.3" sets the maximum tolerance for the control points to be 0.3 pixels (the default is 3 which is too large if there are no good reasons why you shouldn't get almost perfect alignment) , "-c 20" sets the maximum number of control points in each 5 by 5 subdivision of pairs of images to be 20, the default value is 8.
If you add "-p test.pto" to the command, then you can open the file test.pto with Hugin and then modify the control points, do the remapping with different option or make other changes.