Over the years I have tried out (and discarded) a number of reference managers, including Papers for Mac, Mendeley, Bibdesk, and Zotero. Very recently, thanks to a tip by Magnus Carlsson, I finally found one which actually seems to be doing what I want it to do: Colwiz. Here are some of the reasons I like it:
– Articles are stored in the cloud AND on my own computer. I really want both.
– Everything just works, even if you’re not a super-hacker like Andrew Stacey.
– I can easily import (lots of) references from MathSciNet (still not possible in Mendeley, which is why I once posted my angriest online comment ever on their feedback page). For example, I just imported references to all articles ever written by Gillet and/or Soulé in less than a minute.
– Colwiz automatically includes links (via doi and also via MathSciNet) to online versions of the article. I think this is brilliant.
– The desktop application apparently does not automatically mess up my own folders and naming of files.
– It’s free (at least as long as you don’t want more than 2 or 3 GB of pdf articles in the cloud).
– They have apps for iPhone, iPad, and Android.
– It’s designed for collaboration.
So far I haven’t discovered any major drawbacks. I doubt that their e-reader handles djvu files, and it seems (unless I’ve missed it) that you search in your own references on general keywords only, without the option to use fields like journal name, time interval etc.
Finally, some links to related things: A MathOverflow question on tools for organizing papers. Wikipedia’s rather complete list of reference managers. Konrad Voelkel’s blog, where he has written on managing papers, managing metadata, and much more.