If you previously used version 2.x of Thunderbird and upgraded to 3.x (for example through an Ubuntu release upgrade) you might notice that Thunderbird will not show any of your old e-mails or settings.

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This results from a different directory being used for storing profiles and configuration.

You can replace the blank profile with your old one like this:
cd ~
mv .thunderbird .thunderbird-invalid
cp -R .mozilla-thunderbird .thunderbird

Upon its next start, Thunderbird brings up the migration wizard introducing you to a few version 3 features and allowing to revert some settings to 2.x behavior.

Your profile(s) from previous to the upgrade remain inside ~/.mozilla-thunderbird and can be removed if everything goes smoothly.