Comment 10 for bug 899285

For people that can edit files and are not scary to mess things up (always make a backup of the files you like to edit) in this post http://askubuntu.com/a/32919/15917 I found the answer I looked for a long time. There I simply add the "whateverprogram.destop" file to the "~/.local/share/applications/mimeapps.list" [Added Associations]-section, restart nautilus and it works.

This also works with for my wine apps.desktop files, which where not recognized by the system any more (and could not be added manually by the ubuntu-tweak software either).