I know this isn't as simple as it sounds, but I'd love a feature where with say cmd-i I could ask Usenapp to ignore the current thread in perpetuity. Which means effectively pre-mark as Read, I think.
I don't want to kill by subject, as there's too much chance of clash.
Ideally cmd-i would ignore the whole thread, cmd-alt-i would ignore the current message and all its replies.
Even more ideally, the keystroke would be a toggle, marking the thread/subthread as ignored, or undoing that and allowing it to show new messages as unread as would be normal.
I imagine this would work by message-id and references: tree, or whatever internal tree structure you use.