How to annotate/summarize research papers for long-term retrieval?
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.