RegDiff

It is a small command line tool to compare two registry files, export the registry, merge .REG files and much more.

regdiff.exe is freeware with a very liberal BSD-style license (i.e. free for any use including commercial).

Features:
-Compare, diff and merge .REG files
-Compare, diff and merge the registry
-Support for both ANSI and UNICODE style .REG files
-It's free!