In TB 5.0 the hyper-links in the messages don’t work, even with the changes like these they do NOT work:
1) To be absolutely sure: make back up using MozBackup http://www.mozbackup.nl/
2) In Thunderbird, go to Preferences / Advanced /Config Editor (it will warn you, say yes)
3) Scroll down to network.protocol-handler.warn-external.http and make sure it’s set to true
4) Do the same for network.protocol-handler.warn-external.https
5) Do the same for network.protocol-handler.warn-external.ftp
6) Do the same for network.protocol-handler.external-default
7) Exit Thunderbird
8) Restart Thunderbird. The first time you try clicking on a link (or sooner) it will ask you to confirm that you’re using an external handler. Say yes and check the “Always do this” checkbox.
Thanks to Charell.
EDIT:
Recently, with thunderbird 31, the above steps are not working.
To change associated application, edit the mimeTypes.rdf file, placed in thunderbird's default profile folder.
Example: in my case, I wanted to change http(s) associated files to be opened with firefox-aurora, instead of firefox, so I've executed:
sed -i.bak 's/\(firefox\)/\1-aurora/g' ~/.thunderbird/m3e8sg0w.default/mimeTypes.rdf
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