I tried the SpyMe Tools under Windows 7 SP1 x64. You have to do different snapshots for the registry and your files, thats a little bit annoying... (and if you choose an empty password you cannot use this file again later for comparison, so you have to click on "No Password"...). The compare of the registry showed no "moving" status indicator, you don't know whether it does anything or not, I canceled it after 2 hours.
WhatChanged 1.07 was much slower (as it does comparing and snapshot at the same time), and you cannot save the snapshot to disk. You get a status indicator how many entries are compared, but compare took over 3 hours.
I also tried the Windows System State Analyzer from Microsoft, but it didn't work for me (freeze when I'm trying to scan the system).
The last thing I tried was InstallWatch Pro 2.5 (manufacturer site is gone, see here or at google for the setup project). The compare was done in 2 minutes (you can decide whether version infos or crcs of files are compared or not). It finds files and registry keys but has some minor problems with special folders (e.g. tells me that "c:\Documents and Settings" was deleted).