Good chance the file associations for .exe are missing or changed. A couple of viruses do this so that anything you open opens their software. It is a simple enough fix.
Save this as a .reg file then merge it on the effected machine. After a reboot hopefully things will be back to normal .exe wise.
Code:
Windows Registry Editor Version 5.00
[-HKEY_CURRENT_USER\Software\Classes\.exe\shell\open\command]
[-HKEY_CURRENT_USER\Software\Classes\secfile\shell\open\command]
[-HKEY_CLASSES_ROOT\.exe\shell\open\command]
[HKEY_CLASSES_ROOT\.exe]
@="exefile"
"Content Type"="application/x-msdownload"
[-HKEY_CLASSES_ROOT\secfile]
To save it as a .reg file just copy it into notepad and name it .reg and save as all file types.