Was trying to work out how to publish .Net ClickOnce apps on a Linux server running Apache tonight, turns out its pretty straight forward.
All you have to do is add the right MIME types, so in your .htaccess file just add these few lines
1: AddType application/x-ms-application application
2: AddType application/x-ms-manifest manifest
3: AddType application/octet-stream deploy
4: AddType application/vnd.ms-xpsdocument xps