BACK UP YOUR FILES! You do not want to be the graduate student in the horror story who lost all of their data and notes due to a computer malfunction. Current online "cloud" storage also makes it extremely easy for you to work on the same files anywhere you want: at work, at home, at the library, at the coffee shop, etc. Cloud storage also enables you to work on multiple platforms, from computer to smartphone. As an example, with all of my files saved on a cloud storage system, I can read and take notes on my phone while on the bus and pick up immediately from where I stopped once I get to the office.
Important note: Check with your faculty advisor if there is any legal implications with storing your research data on cloud services, especially if your research is sponsored by the government or private enterprise, or otherwise deals with proprietary information or technology.
(UMD) BOX: BOX for UMD students offers free 50 GB of storage with both a desktop syncing app and a browser interface that allows you to share and collaborate as well as review file version history, etc. Regular free storage is 10 GB.
Browser Login: https://umd.account.box.com
(UMD) Google Drive: Claims to have unlimited storage space for university accounts; 10 GB of storage for free accounts. Every student at UMD should have access to Google Drive through their UMD Google email address.
If you use Mendeley, you can configure it so that Mendeley will automatically save all your reference PDFs to a default folder. If you set this folder to be synced with a cloud storage, you will now have all of your readings available anywhere, anytime, and on any platform. Go to Tools > Options > File Organizer and choose to Copy files to a synced folder.
If you want to make Zotero save all of your references to a single folder and automatically rename them, you can install the ZotFile add-on: http://zotfile.com/index.html#features