OK. I recently had a virus that did untold amounts of chaos to my machine. I have managed to sort most of it out, by re-installing windows but it still beeps when I receive emails. Its not the nice beep, you get when you receive emails, its a warning beep from the tower, just a single beep! Why would this happen. I use Mozilla Thunderbird with googlemail.
Go into ThunderBird settings. If the Play a Sound checkbox is checked, Thunderbird will play a small beep sound every time new emails arrive. You can choose the sound Thunderbird will play by clicking the Advanced button, and choosing a sound file on your computer.