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Don't forget the page file. The page file by default is set with a smaller start limit, and a larger end limit. This allows the page file to expand if necessary and causes the page file to fragment.

Set both entries to the higher limit, defrag the disk after cleanup, delete the page file, then reboot the system. The page file will be recreated and most times defragged too.

You can also use Sysinternals (now Microsoft) pagedefrag utility, but it does not work on Vista or Win7 yet. An added benefit is that it will also defrag the registry, and yes, the registry can fragment too.