i hope you all realize i don't have a external backup hard drive. i only have a 2 gb usb flash drive(full do to backup of orbiter folder) and some blank cd's.
My suggestion? Format the USB drive. You can always download Orbiter stuff again. If you really need to keep everything, talk to a friend or family member, and store the files there. Any virus is something to get off your system as soon as you are able. Simply by leaving it, even if it appears to be inactive, you may still be at risk, and if you do any online shopping, that is not a risk you want to take.
I went through backups when my old PC failed. The best I can suggest is go through everything, and sort it into three catagories: Keep, Keep if able, Forget-about-it.
"Keep" is the stuff that you absolutely cannot replace (pictures, movies, school/work documents).
"Keep if able" items are things like save-games for your favorite games, Steam games, Orbiter, and other similar items. Basically, the stuff you can replace if you need to, but would rather not.
"Forget-about-it" items are everything else.
Then, back up everything from the Keep category, rank the rest in order of importance, and back-up down the list until you run out of room.
Or, if you've got $50 to spare, external HDDs are pretty cheap. Wal-Mart actually has some decent computer accessories (hell, I got my laptop there for $300, and I've had no problems with it).