Somehow my latest work laptop (Dell Latitude D620) has a PC speaker circuit that bypasses mute settings and the headphone jack. I was finally able to silence the base Windows XP I have installed, but I still had issues with different systems running under VMWare Workstation. I'd get a nice loud beep on a reboot, Solaris X86 somehow locked up into an ear-splitting squeal, FreeNAS beeps on every boot, etc.
After a lot of tinkering, I finally came across the answer here, which now seems to be a dead link:
Go to the global VMWare settings:
"\Documents and Settings\All Users\Application Data\VMware\VMware Workstation\config.ini"
mks.noBeep = "TRUE"
That finally did it, at least in v5.5.
UPDATE: Ethan says it works fine for v6.0 on Vista except his config.ini was in:
"C:\Users\All Users\VMware\VMware Workstation\config.ini"
Find out what's on Clearance at ThinkGeek!