I haven't collected a paper article in about three years. I actually use the comments/annotation feature in Adobe Acrobat. You can make a comment and later Adobe will go through and create a document of just the comments or annotations (which you can then feed into DevonThink if you're using it). It's great for articles that you teach from regularly. I used to make the same notes on the same articles because I'd misplaced the one I used the last time. Now, it's all electronic and with me all the time. I've also been using Spotlight Comments and Smart Folders to keep articles that pertain to particular projects together. It's not perfect, but it's been working pretty well.

Does anyone else use Adobe this way?

I also keep the .pdfs themselves linked to an Endnote database