I thought I'd blogged about this before, but when talking about with Simon Sabin just now, I couldn't find it.
Simon's just blogged a couple of ways of stopping the beep from the command line. Here's one using a User Interface.
Go to Device Manager, and make sure that "Show Hidden Devices" is checked in the View menu.
Now you can find the Beep in the "Non-Plug and Play Drivers" section and edit its properties (setting it to Disabled).