Like anything else, figure out why you're reading a paper, what are your goals? If you're reading for expanding your knowledge in a field, then a good area to

Like anything else, figure out why you're reading a paper, what are your goals? If you're reading for expanding your knowledge in a field, then a good area to start is by reading well known dissemination in the field in past decade or so. So, say, you're into datastrucures, read the paper that brought Red-black tress by Rudolf Bayer. This is also a great route for somebody reading for the first time. Well written papers are less off-putting. Most papers out there are very poorly written. If you're trying to extend the field, then it helps scouting what interests you in extremely recent, interesting works. You can use sites like arxiv to find edgy works done in past month of so, and then drill down the references to understand where they came from. You can then work on improving that work. So it depends on what you're trying to do. For software, I usually use GoodReader on iPad. Nothing fancy, but it annotates, stores all my research papers and organizes them. On computer, give Zotero a try. If you're at a university, remember to catalog papers you read. It's so much easier now with things like Dropbox. After you get out of the college, you will need to pay huge amounts of money for them, so it behooves to maintain a steady collection safe somewhere where you can always look back to. So catalog what you read properly. Don't get overwhelmed and start losing the PDFs.