Hey Natsteel, I use a lot of these programs too, in almost the exact same way! I have two questions for you, though. 1: So am I right in understanding that you differentiate your use between Notebook and EverNote as you use Notebook for taking class notes, but EndNote for random note taking? (I'm assuming web clippings and the like.) What stops you from using EverNote to take class notes? Preference? Or is there a practical reason I'm missing?
Also, you say that you back up your data to DropBox. Do you do this with EverNote too? If so, how? I've been wanting to do this but I haven't figured out how to manage it
I know this is a little late, but... Yes, I use Notebook for class notes and EverNote for random notes (paper ideas, book lists, and my own reading notes and book reviews). There is a way to back up your Evernote by going to FILE -> EXPORT NOTES TO ARCHIVE. I then put the archive file in Dropbox as it's quite small. Also, I suppose I could just as easily use EverNote for class notes but because I used to record my undergrad classes, Notebook allowed me to drop the audio file (and other multimedia stuff) right onto the note page. I think that by now EverNote has much of the same functionality.
Natsteel, your workflow looks pretty amazing. I am using DevonThink Pro Office, Mendeley, Scrivener, and my boss (I'm a research assistant) uses LiveScribe and loves it. Pair that with ExpressScribe and you're good to go! The question I have for you is: how do you manage the DEVONThink - EndNote flow? I want to use EndNote for the CiteWhileYouWrite but it feels tedious/repetitive to manually put things into EndNote, since I can't find an easy metadata export function from DEVONThink. Do you have any particular reason for using Papers2 over Mendeley?
Also, re: the Windows question, Quiqqa looks pretty amazing and is only available for Windows, so I would use that if I were on a PC. I think it's comparable to Mendeley, and maybe Papers2? Plus seems to have a good annotation component.
Does anyone have a good annotation program? DEVONThink is okay, but not entirely intuitive. Ditto for Mendeley, Adobe, Scim, etc. I want to be able to highlight passages and add notes, and then hit a button and have the highlighted passages and the notes exported to a word document.iAnnotate appears to do it, but I don't have an IPad. Thoughts?
At this point, I have (almost) completely dropped EndNote. At first, Papers did not have citation management (in the sense of CWYW). It has added that to v2 and it is so much more intuitive than CWYW ever was (which was why I never used it). I share some of your frustration with DevonThink. I basically use it as index of my document folders on my HD (for its search capabilities). I do most of my annotations in Papers and if I have a highlighted passage I want the text of, I just hit CMD-C as soon as I've highlighted it and then CMD-V it into the notes section.
One last thing, if you're working on large projects or large research papers, I have found Scrivener to be indispensable. It's incredible for note-taking, outlining, writing, and organizing your research/sources. It used to be Mac only but a Windows version is out now, I think. It was originally made for screenwriters and novelists but with a bit of tweaking it's fantastic for writing and organizing 30+ page history research papers (and even historiography papers). Plus it even comes with an export feature that will automatically format your paper and footnotes to whatever style you pick. I'm an obsessive when it comes to following style guidelines and I was surprised at how good the formatting was. DISCLAIMER: I'm not shilling for the company, but just trying to share an application which not only increased my productivity but changed the way I do research and write for the better.