I commented on this in the Mac thread, but as it is multi platform I thought I'd list it here.
There is a great free progam called Elastix
http://elastix.isi.uu.nl/about.php
It allows some extremely advanced image registration and is command line driven, and the source code is available so you get full control.
I find it very useful, not just for Astronomy but for Feature Film reconstruction, where we can digitise in multiple film sources and align them all with great control.
There are matlab wrappers available as well. Woot!
Just thought I'd throw it out there for all the CLI junkies (You know who you are
)