I'd love to see a "muted" toggle at the top of the thread listing. Maybe under the "new topic" button. It would show that there are muted/hidden threads (when the feature is enabled) and show them when it is disabled.
If not a built in feature for the site, once the features/layout get stabilized, I would imagine that some of our more creative script-authors would be capable of adding such functionality.
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I think this would be excellent. Just toggling certain threads off from view would be great. Then again, you're also assuming that everyone tags their threads correctly.
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I LIKE IT!
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This seems like a decent compromise.