With all the tab-completion and such that I do at the command line, sometimes that system beep can get really annoying. I like to have audio feedback when I'm working, so I didn't want to disable the beep completely, but I did want something that wasn't quite so harsh. I searched around for a while in the preferences to see if I could change things to play a nicer sound file instead of the speaker's beep, but it doesn't look like that's available as an option. Searching the web, I found this post at tjworld.net, which got my system playing the sound file I wanted: XandGnomeSystemBeepWithAudioFile. (Note: there's a misspelling for the xkbevd config file name in that post; it's actually "xkbevd.cf".)
While that finally got a sound file playing instead of the beep in other apps, in the Gnome terminal, it played both the sound file *and* the system beep . . . even more annoying :). In the end, here's what I had to do to get *only* the sound file playing as the beep in the Terminal:
First, in the System->Preferences->Sound preference setter, go to the System Beep tab, and de-select "Enable System Beep".
Next, in the Gnome terminal Edit->Profiles menu, select the profile you're using, then on the Edit->General tab make sure "Terminal bell" is selected.
So, you have to *disable* the system beep in the global settings, then *enable* it in the terminal settings.