How to annotate/summarize research papers for long-term retrieval? I am new to my field (cell biology / immunology) and I would like to ask about the best practice to annotate or summarize research articles and reviews for long-term retrieval. When I start reading into a new topic, I end up highlighting almost each paragraph of the paper/review. This doesn't make any sense, and it is actually making me slow and frustrated and it is holding me from reading more. Could you please share your thoughts.

Update: although two very important points of how to approach new papers and how to tag them have been addressed in the answers so far, my main concern was about the new acquired details which I can't remember a few months later. For example, I read a paper about JAK/STAT signaling two months ago, now I can't remember for example which JAK attaches to which cytokine receptor and interacts with which STAT. I need to skim through the paper again to find this piece of information. So, what I am looking for is an approach to accumulate the new knowledge and to facilitate reviewing them without the need to skim through the paper again and again. I know this will come with experience, but at the beginning there are too many new facts to keep track of.
I find it important to be as active as possible in your reading, especially for papers close to the questions you are working on. If you are only highlighting, then this is largely a passive activity, and does not help much with retention or even later rereading. If you are making notes, it is a little bit better, but still largely passive. 

For important papers, I try to read the paper and then write up a quick summary for myself of the key ideas relevant to my interests: a sort of mini-review or personalized-abstract of the paper. For papers that don't contain important tools I use, but contain facts I have to cite I usually include a section that lists in what settings I would expect to cite this paper. This helps a lot at the writing stage. These little summaries of the paper are usually too rough and critical to be useful to others, so I keep them private. 

I usually organize these summaries in a little personal wiki like Tiddly Wiki where I can tag and do full text search as well as include links to the original PDF of my computer. Each article gets its own tiddle and is tagged according to topic. Other useful tools are available in: 

Is there any efficient non-linear note-taking software?

For some heavy papers (say important math papers) the reading has to be even more active. Usually including reproving the theorems and sometimes presenting these proofs to others in my group.