I make separate folders for each of my WIPs and keep them on my desktop. I give them shorthand names so the titles fit on one line: about 8-10 characters in all. "Frosty The Snowman," for instance, would be chiseled down to "Frosty." Within each folder I have a sub-folder for text and sometimes another for scanned drawings. (Several of my manuscripts and short stories are illustrated.) I'm still searching for a way to better organize my desktop, so am eager to hear how you do yours.