piggy-backing on FoxMom's suggestion, you can use the clear, full sheet labels. It will just about cover the entire folder and give a cleaner look. If you want professionally done folders, you can try vista print, or google "custom printed folders" but it will cost you a pretty penny.
I would get all my papers together and in August Walmart/Kmart and all the retailers put their school supplies on sale-- you can get folders for .10 cents each-- and stock up at that time-- you could get the folders in your school colors-- and make a label/sticker with your school name/logo to put on the cover.
I am working a compiling an info/welcome folder to be given out next fall and throughout the year for new students. We would like to use 2 pocket folders with our school name on the front. Can anyone recommend a company?