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I just noticed on my Macbook that every Tiger window I open there is a question mark at the top not to far left of the search box. It doesn't appear in any application's windows.
Do you mean in the Finder? If so it means you had an icon to e.g. a file or an app in the toolbar and the item no longer exists. To get rid of it, command-drag it out of the toolbar and drop and it will disappear as a poof of smoke.