I've been developing in Flash Builder 4 (under Windows 7) a lot in the last months, and there's a detail that REALLY annoys me: a click sound every time a file is opened or closed, or when a information bubble pops, and in too many other occasions. After going through each and every Flash Builder option, I finally found a way to get rid of that sound with the precious help of our friend Google. Seems this "problem" is related to Eclipse (on which Flash Builder is built), and Windows (no way!). So the way to disable this click sound is by going to:
Control Panel -> Sounds ->Windows Explorer -> Start Navigation
Set this value to "None", and you're done! You don't need to code with your speakers turned off anymore!