This just happened to me for the second time, and as the cure took some time to find in Apple discussions I thought I'd post it here for the good of the community.
What's happened to me, and others, is that the icon for your System HD no longer shows up on the desktop or in new Finder window sidebars, but everything is actually working fine. What's happened is that somehow the "visible" attribute of the disk has changed to "invisible". To cure it, open Script Editor (which should be in Applications>AppleScript) and paste the following:
tell application "System Events"
set visible of disk "NameofDisk" to true
tell application "Finder" to quit
tell application "Finder" to launch
*REPLACING "NameofDisk" WITH THAT OF THE ACTUAL NAME OF YOUR DISK*
Click Compile to check for errors and then click Run. You should be back in business.
I hope this comes in handy for someone, sometime. If it does then please feel free to shower me with praise, cash, slutty outboard etc.