Comment 3 for bug 222944

Alright, so this "works for me" [tm] to fix this problem:

Open firefox and enter "about:config" into the location bar.
Set the filter to "mailto". Locate the "network.protocol-handler.app.mailto" line, right-click and select "reset".
Close firefox.
Open nautilus/thunar/whatever and go to your firefox profile directory (/home/<user>/.mozilla/firefox/<some weird string>/)
There's a file called "mimeTypes.rdf". Remove it (or rename it, if you're the cautious type).
Start firefox again.
Right-click anywhere and select "Send Link...". A window should pop up that prompts you to choose your mailer application. Locate /usr/bin/thunderbird (or whatever is your preferred app). Click ok and the compose window should show up.

For the curious:
If you now take a look at the about:config page, you won't find the network.protocol-handler.app.mailto property anymore. It seems it is not used anymore in firefox 3, however having it still set after upgrading seems to seriously confuse firefox 3.