Zotero can help to organize your research by keeping all your PDFs in one place. You can add these to Zotero by dragging and dropping them into your library. Then, right-click on the PDF and select Retrieve Metadata for PDF:
If it is available, Zotero will then populate the item information for you. You can manually edit and add missing information as necessary.
Check out Zotero's Support page for more tips and tutorials.
York University Library's Zotero guide has additional information that is not discipline-specific.