http://s-k-tools.com/index.html?m_util.html
There's a utility on that site called ssnap which is nice because it can do registry dumps as well as crc32 for files with an option to exclude files in rom. I usually run it off the ppc with the storage card ejected, I couldn't get the exclusions to work properly. The files can be compared in compareit or windiff.
Also, the task manager app that seems to be making it's way into alot of these roms seems to have a pretty decent registry editor as well. It even has the option to export MULTI_SZ/MUI_SZ in "RGU format" although it seems that the hex output by most other reg programs works as well. If you use the rgu format option, strings that contain \, rgucomp complains since these should be double backslash (\\).