My Thunderbird stopped launching URLs in Firefox when I clicked on them. I did some digging and it turns out Thunderbird pulls the browser settings from gconf:

gconftool-2 -g /desktop/gnome/url-handlers/http/command

Mine was incorrectly set to an old invalid path. So I fixed it with:

gconftool-2 --type string -s /desktop/gnome/url-handlers/http/command "firefox %s"