Tools for Organizing Papers? Much like a previous question on keeping research notes organized, my question is how people keep their pile of papers organized. I've got a stack of about 100 in my office, most of them classifying as "want to read", a couple "have read", and lots in between.
 A: I use Bibdesk, and it works quite well.  It's free (as opposed to Papers).  I haven't tried Mendeley, but I've heard good things.  I also use CiteULike to bookmark papers that I'm interested in.
A: As for physical papers:
I have two coexisting systems.  The first is a file cabinet organized by author.  Organizing large numbers of papers by subject or date or whatnot ravels out of control.  The second is a series of magazine racks labelled by project, which contain papers directly relevant to the corresponding projects.
As for electronic papers:
I used to put them in folders by author, with helpful filenames like  
Fukaya-FloerHomologyFor3ManifoldsWithBoundaryI.pdf
HatcherLawson-StabilityTheoremsForConcordanceImpliesIsotopyAndHCobordismImpliesDiffeomorphism.pdf
KustermansRognesTuset-TheModularSquareForQuantumGroups.pdf  
but maintaining this got old.  I tried Papers, and thought it was going to be fabulous, but like Scott, wasn't won over in the end.
But now search has gotten good enough there is much less need for explicit organization.  You can just put the pdfs all together in a ginormous folder, and whenever you need something just search for it.  It's the google way.  (And if you use Google Desktop, then literally so.)
Here is the one thing I would like to be able to add to this system: it would be great to be able to add tags to papers, which would even further facilitate targeted retrieval and browsing.  Does anyone know an easy way to do this?
A: Although I just started using it, Mendeley Desktop seems like a very good tool to organize papers. How to organize the hard copies in the office is still way beyond my knowledge ;)
A: Mac users might find the program "Papers". I tried it for a while, and didn't end up excited about it (maybe I don't read enough papers?) but I've heard good things from many people. 
A: There's a Firefox plugin called Zotero, which is supposed to help organize online research. It can even automatically grab data from sites like jstor, springerlink, amazon etc. 
I have just started using it, does anyone have any experience with it? Is it usable for mathematical research?
Edit: There's a video demonstration on their homepage which really looks impressive!
A: I use a modified version of RefBase.  It's an online bibliography database that can also store copies of papers.  Useful features include:


*

*Multi-user capabilities

*Import from arXiv by identifier

*Tagging and grouping of articles

*BibTeX and other formats exported

*Links to webpages and so forth

*Import from a BibTeX file (so you can pass it your bibtex file from a paper) with automatic grouping


My modifications include:


*

*More mathematical fields (the main developers are geologists)

*MathSciNet import by identifier

*It gets the daily arXiv listing and I can choose which articles to add to my collection


My version is available on github.
A: There is a new tool called colwiz, which seems to have some advantages for mathematicians. In particular, it has MathSciNet support, unlike Mendeley. I wrote a summary of why I like it here.
A: Try this tool.
EDIT: The program is called citeulike. It is a free service (at least as in beer, not sure about speech) sponsored by Springer. It appears to allow you to store, search and tag PDF's and to search others tags. Edit by David Speyer
A: This is something I've been musing about for a little while, without very much progress.  Wikipedia has an article comparing various different reference management systems.  I'd like something that I can access no matter what computer I happen to be using (sometimes I work at home, sometimes I work in the department) so although the Firefox extension Zotero looks pretty good, and is properly extensible, it didn't look like it was going to be particularly easy to use on more than one computer (unless I kept a copy of all the local files on a USB key and remembered to take it with me).  Having said that, the official website says that version 2.0-beta has the ability to synchronise via a central server, so maybe I should take another look at it.
I had a look at a few web-based systems, and experimented with Bibsonomy, CiteULike and Connotea, and vaguely settled on Bibsonomy, but I haven't entirely taken to it.  The social networking aspect appeals - accurate recommendations for relevant other papers would be great - but I'm not sure it's quite there yet.  Perhaps I should follow Andrew's lead and install RefBase on my home webserver.
A: I've found JabRef, http://jabref.sourceforge.net/ , to be the best tool (for me) for organising a BibTex database, and linking / organising all of my downloaded pdfs.
The biggest advantages of JabRef are that it is genuinely cross-platform, being written purely in Java, and that the native format for the database is BibTex, which means that if I decide to change my methodology then I can straightforwardly use my database with other programs. Storing the database as a BibTex file also means that I can directly edit the database, e.g. doing search and replace with an editor.
It has all of the functionality I need, and in particular it is possible to apply labels to each paper for categorisation, either manually or via keyword searches.
