Thunderbird > 4.x on Linux does not honour default browser

Thunderbird (at least version 6 here) appears to be using the XDG MIME actions specification. The preferences are stored in ~/.local/share/applications/mimeapps.list, and all desktop environments are supposed to respect them.

[Default Applications]
text/html=chromium.desktop
x-scheme-handler/http=chromium.desktop

Older versions of Thunderbird may still be using GNOME's Gvfs for this. You can check using gconftool-2:

$ gconftool-2 --get /desktop/gnome/url-handlers/http/command
firefox %s

If that's the case, the best option is to configure Gvfs to use xdg-open for all URL schemes, which in turn should invoke the right program from mimeapps.list:

$ for scheme in http https about unknown; do
    gconftool-2 --set /desktop/gnome/url-handlers/$scheme/command \
        --type string "xdg-open %s"
done

Or you could try xdg-settings, which... honestly, I'm not sure what it does:

$ xdg-settings set default-web-browser chromium.desktop