It seems to me that using inputrc only fixes beeping associated with the bash shell. When I do it this way, the beeping from unsuccessful tab completions goes away, but I still get beeping in emacs and in less for example. You can remove the relevant module (called pcspkr) from the kernel and you'll still be able to listen to whatever you want from the soundcard since, as zchoyt mentions, the beeping's not coming from the soundcard. I have the module removed right now and there is no beeping. That's nice since I listen to the radio with headphones and the beeping is REALLY loud with my headphones. If you decide you need it again you can always insert the module back.
Here's an explanation:
Sorry, there seems to be a problem right now with kernel 2.6.18 so the blacklisting doesn't work with that particular module but the rmmod works. Maybe there's a better way then that doesn't require always using rmmod.