I've looked at OmniOutliner, Yojimbo, Evernote, Scrivener and Zotero. I use and love Zotero and Evernote for other purposes, but they don't quite do what I want to do for research. I can't be that weird - I imagine there's a lot of folks in academia with similar interests. I want to read research articles and take notes on them. But, then later, I want each individual note to be organizable into my paper flow but still linked to the reference they are from. That's the catch - all the above allow you to organize notes under the item, but then you can't rearrange them independently of that structure. For example, say I have two articles: Article 1 Note A Note B Note C Article 2 Note D Note E Note F I want to be able to drag my notes (each line a separate note) into my writing outline. Topic 1 Note B Note D Topic 2 Note A Note C In all programs I've tried, rearranging the sub-notes is either impossible (Zotero) or loses the original reference (the others). One way is to use Evernote's tagging features, but this requires entering the tag every single time. I'd really like to just take sequential notes from a single reference by entering the reference information, and then, every time I hit "enter", it creates a new note linked to that reference, but independently movable. Any ideas?