Software: Managing references

You read a paper three days ago and now you want to dig up the citation for an argument, or for that footnote you forgot to include. Can you find the paper again? If you've been managing your references well, you might be able to! Luckily now you have software options.

The tool I've used longest is Zotero, a Firefox add-on. Zotero keeps a "library" and lets you create infinitely nested "collections" within the library. That means you could have a collection for each class, for each subject, for each body system, whatever. When you come across a paper you like on PubMed or dozens of other databases and libraries, you click a button and Zotero adds that paper (or book or article or record) to your Zotero library. It recognizes authors, titles, keywords, etc, and you can add your own tags and notes. You can also grab a snapshot of the page for off-line reading, or even PDFs. Since I beta tested Zotero, I've gone back and forth with Zotero developers a few times trying to work out issues, and they're very cool and very responsive.

Favorite features:

• integration with Microsoft Word or Open Office -- add a citation in the format of your choice with 3 clicks
  
• highlight text and right click to add a note to your library, which conveniently also carries all the information about the original page, so you know what you were looking at at the time
  
• Saved Searches in the Collections window, like the Smart Folders in OS X. I have Smart Searches defined to show me only those articles with "emedicine" or "mdconsult" in their URL, since those are sites I use often in my current classes

Recently I started using Connotea, which works on similar principles (in terms of recognizing that something is a title or author), but it lives online instead of on your computer. It's like del.icio.us for researchers, clinicians and scientists, complete with tags, user groups, and being able to see who else is interested in the papers you're interested in (if you designate the listing as public). Connotea is a little further behind Zotero on features -- they're still working on an export to a simple MLA/APA/Chicago manual format, but you can already export to other citation managers or BibTex. But if you're looking for an easy-to-access, easy-to-share reference manager, Connotea might be the tool you're looking for.

Favorite features:

• links to other users who cited the same paper
  
• user groups, so you can easily share references with friends
  
• can handle info: links

How do y'all organize all the papers you read?