I'm looking for a non-tedious way to make the Messages application in Mountain Lion silent without killing the audio output of other applications. Any ideas? Is this a job for AppleScript or defaults?
You can change this setting in the Messages app preferences.
Go to Messages-> Preferences -> Alerts. Select 'Message Received' in the Event menu and uncheck the 'Play a sound' box.
You may also have to do this for the 'Message Received in Active Chat' and 'Message Received in Chat Room' events, as well as any others that are triggering unwanted sounds.