It is important to know your way around your "My Documents" folder, and know where files are. No matter how you organize, by class, or by project, you want to be able to access your files on a moment's notice. An important step to having an organized hard drive is naming your files wisely. Having a "My Documents" full of Doc1.doc or "work.doc" files is NOT productive.
If you are in a rush and have to save your files quickly, you may be tempted to give it a short name, with intentions of returning to this file in the near future. However, this is a bad habit, and can lead to cluttered document folders.
While I encourage you to file all of your documents properly in the start, sometimes you simply have to save. That, or you believe that the file is temporary and intend to delete it soon. Saving files to your My Documents folder is okay, but you need to be sure to properly name them. Any non-temporary file should be filed properly so you can re-access it when desired.
So next time your tempted to just name your note "work" or "math calcs", try giving a longer and more descriptive filename. You will be surprised at how much easier it will be to archive or find your files once your done.