In my friends case it was the ability to open files that ended in exe that was affected.  What are exe files, well simply almost any file that is used to install, start, or open a program is an exe file (So they are kind of important for the purposes of using your pc).  He would see this message when he tried to open anything that was an .exe file

     The solution for this problem (and of course for every problem there is always a solution), which was not to reinstall windows came in a small registry file that puts all the .exe settings and .exe “open with” file associations back in place.  In case anyone else runs into this issue, here is the file that fixes the issue.  Just click on the folder below to download the file (Because this is a registry file, your pc may alert you to a security warning, just click on allow if it does).    

.EXE fix download (http://cid-8804db538b4de88c.skydrive.live.com/browse.aspx/.Public/exe%20Fix)

      Once you download the file (just save to your desktop or other easy to find area), double click the file and you will add a message that says

(Note where my file says \XPMUser yours will have the name that your signed on to the pc with) click on the yes button.

You will now see a message that says

click ok…..and that is all.  You should now be able to open .exe files without being prompted