Academic Note Taking
I am constantly trying to find a good fit for me in reading journals, taking notes, and so forth. I don't like friction and I've gotten to where I detest proprietary files. Think about opening up old WordPerfect files. (I didn't know WordPerfect was still around until just now. I used to LOVE that program when X-Files was on t.v.)
For reading everyday PDFs I use Evernote and PDF Pen Pro. Personally I think that Preview is much nicer, easier, and cleaner than PDF Pen, but the lack of syncing with iOS bugs me. So I use PDF Pen, which is pretty ugly (my taste). My mainstay for PDFs are for academic reasons and for that I use Paperrs3. I've tried both this and Mendeley and I abhorred what Mendeley did with my library. I tried Sente and didn't like it any better.
However there is a fly in the ointment. All notes are not searchable. Searching for some key point in a study that sorta jogs my mind while I'm sitting on a park bench with my iPad or iPhone while writing a plain text document where I am trying to connect the dots between concepts and application in real life is just too much friction in the process for me to maintain creative, broad thinking.
First, I write everything in plain text. Why? Because I like simple and clean for starters. Also I like to try new apps that work great. Because I use plain text I can open a document in Byword, Ulysses, Elements, Drafts, Writing Kit, BBEdit, Daedalus or any other plain text app, depending on what I am doing.
I tried a workflow that was brought up in MacPower Users episode 100, using Skim to pull out highlighted portions of a PDF in Papers2 and attaches them to the PDF and using DevonThink to search. This looks like it would be extremely powerful. Yet it was just entirely too much friction for my little brain which struggles enough with - SQUIRREL- to begin with. Too many steps to get something done is a very un-Mac way of doing things. That's Microsoft thinking, and why I hate it.
So for now I take notes on iPhone or iPad with Drafts, which has some extensions to send it other places. It also does a good enough job rearranging sentences, changing cases, and other workflows that I no longer really ever use OmniOutliner at all. I can then export straight to a note, or copy text (rich text, markdown, whatever) and paste it anywhere.
For reading on the iPad, sometimes Kindle and/or iBooks don't allow one to copy text (though you can do this on the desktop client). This stinks. Nobody has really figured out books for us nerds that like to keep lots of notes and connect the dots. So I take pictures and paste it into the Evernote.
Whether I take a screenshot and paste it into Evernote, or I take a picture with my iPhone of a paper book, I still put it in Evernote. I can annotate on the image in Evernote, adding highlights and such. Plus Evernote has OCR, which helps a lot, especially with Evernote's Context in search.
If I am REALLY in the zone and taking notes, I might have my MBP open. I'll take a picture with my iPhone of the book, send it to my MBP via Airdrop, accept it on the MBP, and drop it into the open Evernote. Then I hit the fn key twice, opening up the dictation, and I'll ramble off some thoughts about the passage. This way I can see a passage, put it in Evernote, rap about it, and get back to the book without losing steam.
Though I do love all the Apple office products, for writing I have made the jump to Ulysses. It is simply gorgeous. It is elegant, has very little in the way of friction, gets out of my way, and because I write it in plain text using Markdown, I can export it to a variety to styles in PDF, HTML, EPUB, TXT, Rich Text, and more.