A quick tip for other Motorola Atrix owners suffering from unwanted notification sounds when connecting the phone to PC via USB.
Simply download a silent MP3 (I used this one) and save it to sdcard\media\audio\notifications
Then go back to the home screen and press Menu > Settings > Sound > Notification ringtone and choose your newly downloaded silent.mp3.
If you still want audible notifications in your apps, then set those up individually within the app.
Why Motorola didn’t see fit to provide a disable feature is beyond me!
(this tip was originally from the Motorola Owners Forum)