Organizing and Managing PDFs and References
Organization and administration is an ever increasing part of any academic’s or researcher’s life. It begins as a small piece as an undergraduate and initial master’s student but grows almost exponentially over time. Luckily there are numerous programs to help manage the academic’s electronic life. Below is a list of programs and some useful links. Here is a link to one rather negative review of a variety of programs. You can find another summary of programs here. Also see these recommendations and this link for a nice comparison of the programs.
Papers – organize your .pdf files like iTunes does for music (mac
Mendeley – A great reference manager that I recommend for people who aren’t Mac uses and therefore can’t use Papers. It is better at linking to PDFs than Endnote.
Zotero – another excellent reference manager. I have less experience with this than the others but it seems very nice.
Endnote – citation manager that has been the standard for academics. Excellent for citations and you can link to the PDFs but it’s not great for managing your PDFs like Papers or even Mendeley.
Bibdesk (Mac only, oriented for LaTeX)
Refworks – no experience with this one
Labmeeting – I haven’t tried this yet since I just came across it but it looks interesting. Drop me a note if you have any experience with this.
*There are so many citation/reference management programs available now it is difficult to choose one. Here is a Wiki with info on dozens of options. Personally, I am using Papers and Endnote
Please join the conversation and tell us about your experiences with these or other programs. Let’s not all suffer in silence.
Daniel J. Hocking 
I've been using EndNote for 6 years now (using X4.02 now). While it takes a bit of effort to keep it up t date, I've found it pretty good as a PDF database. I generally go to Scopus to get multiple citations, and use their export PDF feature to download multiple PDF files at once. I think I have come to like the "Smart Group" feature more than anything, so that I can create literature groupings based on relevant terms/criteria. I'm too committed to switch anything else now.
I had linked many of my PDFs to my endnote citations but then I switched to a Mac and since the directory location was now different none of the links worked. The PDF linking function was very clunky at the time so I never redid it. Papers is amazing for organizing PDFs. It really is just like iTunes but for PDFs rather than mp3s (or other music files). Papers has smart groups and various grouping functions that make it really nice as well (I guess that's new with Endnote since the last version I purchased – 2.0?). The problem is that the citation part of it isn't good. It's really a file organizer rather than citation/bibliographic software even though it has those capabilities. Mendeley seems like it might be a nice all-around solution. Although, I did just get an email from Endnote about their new version for Mac and it seems like the PDF database management part of the program is much improved. I'm not sure I'm quite willing to pay for the Endnote upgrade but I'm rather frustrated with my current lack of organization or at least my piecemeal system. It'll take some serious time to get everything straightened out and I'm procrastinating while I try to figure out the best system.Do you use Endnote on multiple computers or ever use the web version for working on a different computer?
I've been using Mendeley and I like it so far. It's easy to keep my PDFs organized, and it's easy to search by author, which is what I find myself doing more often than not. I know there's a "folder" option, so you can arrange papers by subject, although I haven't tried using it yet. Ideally I'd wish for something more along the lines of tags, so you could assign each paper to multiple topics. I tried using it to create citations in a Word document and found it pretty non-intuitive, but I'm hoping that with more practice I'll figure it out. It's nice too because they also store all your PDFs online, so if you had a PDF emergency away from your own computer you could still access your library remotely. All in all I recommend it!