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This used to happen only if I do it before Ubuntu was fully loaded or if it was just waking from a suspend, but now it started happening always. My laptop is Acer Aspire 5740. Can the OS suppress this beep?

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If you remember or if you have windows installed does this happen there? (When I Google the laptop I noticed that it came with windows 7 64-bit.) What Ubuntu version do you have? – Alvar Apr 3 '11 at 19:49
up vote 1 down vote accepted

To remove the PC speaker driver type sudo rmmod pcspkr to add it again sudo modprobe pcspkr.

In Addition try System -> Preferences -> Sound and select the System Beep tab. Then de-select the system beep.

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Not related to OP's question, but I don't see a System Beep tab under Sound on 10.10. What version are you using? – Ankur Banerjee Apr 3 '11 at 20:44
Thanks, muting 'Beep' from alsamixer did the trick for me. – sashoalm Apr 11 '11 at 9:15
I’d like to enable the warning beep when power is unplugged, but sudo modprobe pcspkr didn't do it for me. Ubuntu 12.04 – isomorphismes Apr 22 at 17:34

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