For Opera it worked when i added the following to the .desktop file:

MimeType=...;x-scheme-handler/http;x-scheme-handler/https;

Something similar would propably solve the problem for the other apps.

However, there should be a possibility to set the default app via
gconf/dconf. If i change it there the change is reverted when opening
gnome-default-application-properties...

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https://bugs.launchpad.net/bugs/708382

Title:
  cannot create "custom" preferred applications

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