I've always been annoyed that the only way to mark all as read for a mailbox in Mail was with a contextual menu in the sidebar. So I wrote a simple AppleScript to do the job:
tell application "Mail"
activate
get message viewer 1's selected mailboxes
repeat with thisBox in result
set read status of (messages of thisBox whose read status is false) to true
end repeat
end tell
I use
Butler (but any such tool capable of creating macros would work) as my quick launch keyboard macro tool, and I've assigned the above script to run when I press Command-K (to match my NetNewsWire usage).