Zotero is a powerful tool for managing any research project. It has many professional features (there are more than 7,000 CSL-based style templates to ensure you get the citation format you need), but the core of the program is simple enough for anyone to use.
Once you've set everything up, for instance, adding some web reference is usually as easy as clicking a button in your browser (Firefox, Chrome and Safari are supported). The link will appear in Zotero's library, and you can then add more, or import local files just by dragging and dropping them onto the program.
Each of your references may be annotated with text notes, tags and more. You're able to organise them into "collections" (folders, basically). But the best part is most of this content is indexed: type a word or two in the search box and it scans your web content, local files, notes, tags and more, listing any hits.
Your research library is stored centrally, on Zotero's servers. You have to create a free account to set this up, but it only takes a moment, and they don't need anything more than your email address. And once it's done you're able to view your current research from any device, access files or links, add notes and more.
Anyone writing an academic paper on all this can quickly generate bibliographies, properly formatted citations and more, mostly just by dragging and dropping (the program includes Word and LibreOffice/ OpenOffice addons to make the process easier).
The only real issue here is that Zotero's free account offers a mere 300MB storage space, not a lot if you're hoping to add several chunky PDFs. Basic upgrades aren't cheap, either (even 2GB costs $20/ year), although you can opt for unlimited storage for $120/ year.