Upgrading to Jaguar causes the /opt folder to be invisible to the Finder -- It is still intact, you just can't see it from the desktop.
To make it visible again, do the following:
Open a Terminal window.
Assume the root ID by entering:
Enter your (Mac OS X) Administrative password when asked
Change to the root file level:
Edit the .hidden file with pico by entering (note the dot before the file name):
with the arrows, navigate down and delete the line containing:
save the updated file by entering:
Exit pico by entering:
Reassume the cfmx user ID by entering:
From the Apple menu select Force Quit... (or press Command+Option+Escape).
Select the Finder and click Relaunch
When the finder is relaunched, you should see the opt folder on Macintosh HD, just as it was before installing Jaguar.