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Tag Toolbar v0.8a4, which is a test version for Thunderbird3, has a new system category "Recent Tags". See the category list in the Tag Toolbar. You can find "Recent Tags" category in the bottom of the list. It records 5 recently used tags by default. Of course, you can customize the number of tags to be remembered in the option dialog.
It is one of frequently asked features. It is useful feature for power users who manage tons of tags. Of course, I know there are users who do not need it. If you don't need it, input 0 for the number of recent tags in the option dialog. "Recent Tags" category will disappear from the category list.