Oh roweski, you are NOT alone... me and many others on other forums have had the same thing happen, many people are astonished by the fact that it's SO random and even Apple has no idea why it happens or has any fix to it! So frustrating.
So to add my story to the ever-growing forums on this topic (I will be publishing the same text to a few other places, in the hopes Apple will post a response!)...
In our case we have 5 computers and printer on a wired network. One employee was trying to print out of InDesign CS3, and print failed. Looked in the print tray and found it had printed a "Network Configuration" sheet because it had lost the link to the network. So we of course tried to see why printer wasn't working, which is when an employee notice the question marks on some dock apps. Upon inspection of the application folder, she found ALL Adobe CS3 apps were gone, as well as Firefox and Excel. Of course we were freaked out and upon further inspection we found (as others seem to have also found) that all files accessed that day (about 14 files, Excel, Illustrator & InDesign files) were also GONE. The only other odd thing was that there were a couple folders called "Recovered Files", one on desktop and one in Trash, but upon restart, theses disappeared and what was left in Trash were about 27 files from the previous week.
We were able to restore most items via Time Machine, but as everyone has mentioned, we NEED to know WHY this happened and how to prevent it happening again. And for the record, we have NOT recently run any Apple updates. PLEASE if anyone has figured it out, let us all know. And if not, please mention what you were doing at the time or shortly before you noticed the problem. Many people have said it "sounds like a virus" but if you search this, you'll find that there are no known viruses of this sort targeting Macs.