Do you have the Wine PPA installed?  The default Wine packages make use
of cautious-launcher but the PPA ones disable it.  Wine's mime type
should cover .exe and .msi at least, I'm not sure what happens to .bat
and .com files as it's been so long since I've seen one.

Cautious launcher is part of the mime-support package.

Regarding 2): We absolutely do not want root permission for scripts that
A) the user has already given permission to be executable by marking the
execute bit and B) are user-level scripts.  Asking for a password there
is wrong; running it (since it has permission) is right.

-- 
Shell scripts require execute permission to execute
https://bugs.launchpad.net/bugs/652470
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