Making it easy to run Windows applications in Ubuntu also opens the door for all the Windows viruses and worms. So why not scanning Windows applications for viruses automatically? With the ClamAV bindings for python this is an easy task.
The winelauncher.py could be used as mime type handler for all Windows executables. If the file doesn’t contain any viruses it would be marked as executable and started under wine after confirming a short dialog.
What about integrating lintian into gdebi for third party Debian packages?