I recently got nailed with a virus which infected a bunch of system files, and possibly some of my own. I wish I could have gone back and found where it had written stuff and which files it had contaminated.
It would be useful to be able to put the static Windows files and folders at the top of the disk, and do an MD5 on all of them while you're at it. You could carve out space for the pagefile and hiberfile and use them as a buffer between that which is static, and the rest of the disk. Once optimized, you could very likely provide an optional utility which would detect any attempt to write new data into the static zone. You could also provide an option for users to configure the 'static files and folder' template to include new stuff (we) install later, and want to make sure it's left untouched. The MD5 option would enable Defraggler to periodically check the static area to see if anything was changed.
This wouldn't really be all that hard to do: just provide Defraggler with a '-static_list:<file>' option, and have it go to work re-positioning things. Also, for general optimization features, add a folder in the DF install directory which could hold 'spacer files' placed at strategic locations, thereby enabling it to quickly re-optimize pre-defined disk regions by releasing spacers when doing so would avoid having to move a very large file. (Obviously there would have to be a user friendly 'clear spacers' option somewhere in the mix.)
Windows system restore is one of the few things they've done which I've liked. However, it is still a very cumbersome system, and it has a primary defect in that it dumps restore points off the back end. Furthermore, in my case, the malware wiped out the restore data. If you implemented the above, Defraggler could provide the ability to snapshot the system periodically, and then store a perfect copy of the snapshot on an external media, which could be used to restore the system to perfect working order later in the event of a problem.