lost desktop folders and files

I was using Eclipse last night on my eMac with a text editor (mi), Safari, and Mail running. Nothing very fancy, At one point when I minimized the Eclipse window, I saw that most of my desktop files and folders were gone (~6Gb). I opened a terminal window and they were'nt visible from there either. I know this sounds pretty stupid, but I am at a loss and therefore willing to take the risk - anyone have any suggestions?
TIA, Mark