Many months ago I promised to write about how I organize my scientific literature horde. The process I've developed works really well for me, and it successfully got me through dissertation writing.
I use Mendeley, a great cross-platform reference manager. I like Mendeley because it syncs across desktops, has adequate annotation features, and works well with bibtex. One of my favorite features is the 'watch folder' option, which periodically checks a designated folder for new additions. I set this option to watch an "add_to_mendeley" folder where I store all PDFs the minute I open them. That way everything I read gets saved, and I'm not left trying to track down a reference online that I have only a vague memory of. Another key setting is turning on automating .bib updating, so my .bib file is always my complete library.
When I'm reading a paper in Mendeley, I highlight and add notes as needed. But what I find more helpful is to write a 2-3 line summary of the paper in the Notes section of the Mendeley interface. I also add any thoughts I have about how it relates to my work. I might say "Model structure useful for spillover events," or "Their findings [x] support our previous findings [y]." Sometimes the note is simply "not relevant", but that's still a helpful reminder not to waste my time when I stumble across it again.
When I'm reading a paper, I also make sure to double check that the automatic citation generator got all of the fields correct, and I add a bibtex citation key if there isn't one already. I star papers of particular relevance so I can find them again easily. I don't usually bother sorting my papers into folders, since the Mendeley search feature works really well. If I'm doing a lit review in a new field I do sometimes go to the extra trouble to sort, because I do more browsing of the collection, whereas when I'm working in my subfield I usually know which paper I need. When I'm ready to write, I just add my .bib file to my latex document, and cite away.
"Send me your data - PDF is fine," said no one ever
The public health paradox ("When public health works, it's invisible")
Let's make data a civic right
Scholarly impact of open access journals
Six months later, disease detectives still battling fungal meningitis outbreak