Zotero is great for organizing and annotating papers, keeping notes, and building bibliographies.

You can create libraries and sub libraries according to topic, and also create libraries for projects or reading lists. Can also create shared libraries, for your research team to share annotated papers.

Finally it can archive offline copies of web pages, which makes it useful for blog articles and other online resources that might vanish.

There's a little learning curve, but it's worth it if you find yourself juggling dozens of technical papers! Enjoy!