Up until Mozilla Thunderbird 3.0, the MacOS version would show you the number of new messages in Thunderbird since you last clicked on the window, in the dock icon. Now by default it shows you the total number of unread messages, which is pretty useless if there are just a ton of messages in your bulk mail accounts you have no intention of reading. A bug report was filed for this issue, in order to restore the old functionality (or at least make it optional). Although the bug was closed and the option was added to Thunderbird, it’s not in the main user interface. It must be set using the advanced configuration editor.

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