While it's not an app, I agree with those who said just folders. I had a folder for each year of college, and within the folder I had folders with the name of each class. Within those you can make folders if there are well defined different projects throughout the class, like I had a lab class where we did a different lab every week and wrote it up, so I had ten different experiment folders within that class folder. It all worked out very well, plus it's clearly laid out if I decide to look back on it later - I won't have to figure out anything about how I decided to organize stuff. You can also back up the folders to flash drives and stuff and have them anywhere, which an app wouldn't be able to do for you... I guess it could make a backup to a disk but it wouldn't be exactly the same as what you have on your home computer.