Thanks Biochembelle @ Dr. Zeek!  Brian's right that older versions of Mendeley on non-Windows platforms occasionally had issues, but those are relatively old and resolved.  I'd love to hear what people think about the new release that just came out today. http://mendeley.com/get-mendeley (pops)

I'm glad they finally got in the game with that, I've been using Papers for the past two years because of that.  Might be time to bring all my stuff onto EndNote then.

TJ, are you running X4

Nikkilina, what version of EndNote are you using? In the latest version you can open up your EndNote library and drag the PDF icon of interest over to the publication of interest and it's inserted. You don't even have to open up the EndNote record you want to insert the PDF into. Viola!

I LOVE Mendeley as well!  Esp when I want to read references at home on the laptop-- I can synch the laptop and the desktop at work and voila! There they are.  The only issue I have with Mendeley right now is when trying to insert/cite in Word- you can't change the bibliography (i.e. if you wanted reference 1 to have a, b., and c.), and it did crash my document once while I was trying to figure out how to edit things in the biblio.  But since I am a masochist and like doing my references by hand anyways, Mendeley is awesome.  The highlight/note feature and serach functions are fantabulous!

I use EndNote and Adobe Acrobat for PDF management.

EndNote keeps track of all of my references. I download PDFs from the internet and then can drag-n-drop them into the specific EndNote entry for that publication (helps cut down on the drag of manual entry). I use Adobe Acrobat to keep track of all of my comments, highlight sections, etc etc. Between those two programs, I'm steadily moving to an electronic office.

I use SCOPUS to download my PDFs, and SCOPUS will rename the PDFs for me if I choose to download them through their own interface.

I and if memory serves me correct maybe Geeka run a hybrid mix of EndNote and Papers.  I generally keep references in EndNote and my PDFs and notes for the articles in Papers so that I can sync them with my iPod Touch and I can navigate papers much more quickly than EndNote to get to my journal articles.

I'm trying to use digital more these days. I really love Mendeley for this (in fact, I've been meaning to write a blog post about it). You register for a free account online and download a desktop client. You can import refs from pubmed or many journal sites through the web client and widget. On the desktop version, you can load PDFs directly into Mendeley. The PDFs don't need specific file names (e.g. PMID in iPapers), and it does a decent job of parsing info from the files. It also picks out ones that don't look quite right or have missing info so you can review and update as needed.

Sometimes hard copies are nice to have around, too. In grad school during a forced massive lit review, I organized all the papers in 3-ring binders by subject/principle, then by year. I also kept a notepad where I jotted down citation and the major finding(s) of the paper so I'd know which one to reference. For me, just doing file folders is not very useful.