1. Label your files in a clear and systematic way: e.g. 'author, date, shortened title, keyword.' Don't let "0115abscd%68.pdf" files pile up in your folder.
2. Label your own documents clearly as well! "Paper.docx" is not going to be helpful in the future. Proudly display the paper's title or chapter's name in the filename as well as some way to indicate the version of your document.
3. Keep track of your versions. Whenever you send your writings to someone else, don't keep working in that same document. Make a new copy immediately and make changes in there. You want to be able to refer back to the same version that you sent out, even if your professor takes 3 months to get back to you.
4. Don't be afraid to use folders and subfolders.
5. Back-up your files with a cloud storage service, such as UMD Box or Google Drive.
6. Digitize your handwritten notes or any paper handouts with your smartphone's camera or scanners available in the Libraries or across campus. With current OCR technology, it's often possible to scan handwritten text into searchable digital text, which can be quite useful when you find yourself looking through course work or a project from years ago.
7. Develop a key for annotating and note-taking while reading. For example, you can use yellow highlight for main points, green highlight for things you agree with, red highlight for questions, etc.
8. Keep a running and up-to-date bibliography that has as many reference details as possible, especially URL or DOI (you never know when a new version of your discipline's citation styles will require it!)
9. Consider using citation management software (such as Mendeley or Zotero) to organize your database of references. This will also automate tips 1 and 8, because citation managers can automatically rename your files and sort them into folders.
10. Schedule a weekly time to organize your notes and readings, with tasks such as moving files between folders, updating keywords and tags, renaming files. In addition to this being a good practice for your organization, it is also a great way to productively procrastinate!
BONUS: Don't be afraid to ask other graduate students and faculty members about their approaches to organizing their research! They can provide you with new ideas on how to make your workflow work for you.