I recently stumbled into an issue of which a ClickOnce application was not started when trying to open it using a browser (doesn't matter if it was Internet Explorer, or Google Chrome, or ...). An XML file was always visible in the browser.
After doing some reach, I noticed the .application file was served as content type: text/plain
We have an older version of Apache HTTPD running (2.2.8, with a release of 2008-01-19). In the $APACHE_HOME/conf/mime.types file, there was no mentioning of the content type for files with extension: application. In a more recent version of Apache HTTPD, the mime.types already takes care of these files.
After adding the following lines (and restarting the Apache HTTPD server), the problem was solved
application/x-ms-application application application/manifest manifest application/octet-stream deploy