It's always cool to read about people's workflows.
For me: working largely with articles, I do a detailed outline, interspersed with quotes and comments (bolded) in whatever I'm using to organize the pdfs--at the moment, Papers as an inbox and Endnote for long-term storage and Word integration. That way when I come back to the article, I can read my abstract instead of the whole thing. I've never made the transition to putting this info into Tinderbox, since I've never put in the time to have Tinderbox emulate the pdf-management facilties of these more specialized programs.
Tinderbox holds
my workproduct--basically, anything with value added by my brain. These notes are about what happens when the article I'm reading rubs up against one of my large/sprawling/ongoing or proto-article/focused/due-dated projects. Depending on what I'm doing in the particular Tinderbox document, these notes might get a specific prototype (like "to do" or "top priority" or "source"), but generally, they're just notes, stuck into the document or container for the project.
I know I'm missing out this way on the discovery of "related notes," but for some reason those serendipitous connections just don't do much for me. In fact, even with my own notes probably 80% end up in the archive, never really re-used! But the
act of making the note--that really makes a difference.
Awaiting Tinderbox on the iPad

at the moment I'm pasting quotes and making notes in a Dropbox-synced set of plain text files, using Notational Velocity on the desktop and Plaintext on the iPad, and uploading relevant ones every so often into Tinderbox. Having multiple syncing services (Simplenote, Kindle, Carbonfin) was messing with my mind.