AIR is a program for image registration written by Roger Woods at UCLA. It is regarded by many in the medical imaging community as the "industry standard". Dr. Woods has compiled a very comprehensive and informative AIR web-page.
Internal (LfAN) links:
The LfAN's AIR page has a tutorial, hints on file-formats, and LfAN-specific information for AIR.
There are a few introductory cartoons that show some of the basic manipulations required of the reslice part of any coregistration program.