A new feature from Gmail Labs solves this problem: enable Hide read labels and "the visible labels in the navigation bar will be hidden under the 'more' menu when they don't contain any unread conversations".
Since the feature only hides visible labels, you can go to the label management page and click on "show all" next to your labels. If all your labels are visible and Hide read labels is enabled, Gmail will only show the labels that include unread messages.
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Google Reader has a similar feature: if you click on the arrow next to your subscriptions and select "show updated", you'll only see the folders and the feeds with unread items.
{ via Gmail's blog }
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