I'm a younger researcher so I have no personal advice, but I have found this method by Michael Nielsen quite effective.
One unusual but very useful style was to set a goal like reading 15 papers in 3 hours. I use the term "reading" here in an unusual way. Of course, I don't mean understanding everything in the papers. Instead, I'd do something like this: for each paper, I had 12 minutes to read it. The goal was to produce a 3-point written LaTeX summary of the most important material I could extract: usually questions, open problems, results, new techniques, or connections I hadn't seen previously. When time was up, it was onto the next paper. A week later, I'd make a revision pass over the material, typically it would take an hour or so.
I found this a great way of rapidly getting an overview of a field, understanding what was important, what was not, what the interesting questions were, and so on. In particular, it really helped identify the most important papers, for a deeper read.
For deeper reads of important papers or sections of books I would take days, weeks or months. Giving lectures about the material and writing LaTeX lecture notes helped a lot.
In particular, I found his opinion on identifying useful material mirrored my own:
Most material isn't worth spending a lot of time on. It's better to spend an hour each seriously reviewing 10 quantum texts, and finding one that's good, and will repay hundreds of hours of study, than it is to spend 10 hours ploughing through the first quantum text that looks okay when you browse through it in the library. Understanding mathematics deeply takes a lot of time. That means effort spent in identifying high quality material is often repaid far more than with (say) a novel or lighter non-fiction.
The whole comment is definitely worth the read.
As far as managing your materials go, I have yet to find an application as useful as Papers. It hooks into your institution's library proxy and allows you to get at licensed content quickly without VPNing in to campus. It's also great for organizing papers by topic and searching over your library via author, title, conference, etc. Unfortunately it's Mac OS X specific. I'm curious if anyone has experience with alternatives on other operating systems.