Recently I saw an interesting error on a client workstation, every app that the user tried to run would bring up a "Open With.." dialog box. I also noticed that running Run > regedt32 would cause a "open With" box to pop up.
The machine had just been recovered from a Virus infection, so I had a hunch this was a setting in the specific users registry settings. To start, you can bypass this by first going to C:\WINDOWS\system32. Find the regedt32.exe file, right click and choose "Run as". Uncheck the box for "Protect my computer and data from un-authorized...".
Now I could open the registry editor.
Next, lets see if the association had been broken. Open "My computer and choose from the top Menu Tools > Folder Options > File Types Tab. Add an association for exe, click advanced and then choose "Application" from the drop down list. Now, lets see if it worked, Press Windows + R and then type cmd in the box and press enter. It should now work.