I’ve read with paper and pen, but these days if I am taking notes while reading, I use GoodNotes and a 9.7” iPad Pro with the Apple Pencil. I don't know how many times I've been working with someone and wanted to check my notes but didn't have the right little notebook with me. That's no longer a problem.
There are three elements to this way of reading: print text, lexicon, and iPad. If I'm reading Greek or Hebrew, I prefer to read from a print text — NA28, BHS, Loeb, or a reader's text. I don't mind reading on my iPad, I just prefer a print text for this type of literature.
It's a different story for the lexicon: about half the time I use a digital lexicon on my iPad and other times I prefer a concise, print lexicon. The lexicon varies depending on the medium.
If I'm using a print lexicon, then it is either Clines' Concise Dictionary of Classical Hebrew, Danker's Concise Greek-English Lexicon of the New Testament, Liddell and Scott's Intermediate Greek-English Lexicon, or for the Septuagint, either LEH or Muraoka's.
If I'm working off my iPad, then it's either HALOT and Clines' CDCH, BDAG, or LSJ in Accordance. It's never really just one, and that's the big benefit of a digital lexicon — you can easily switch between HALOT, BDB, CDCH, and DCH.
GoodNotes is the distinctive feature. GoodNotes allows me to reap all the benefits of taking notes by hand, while simultaneously storing my notes in a digital platform I can access anywhere. The cherry on top is that GoodNotes automatically recognizes the text of your notes — even cursive — and you can search them. Unfortunately, it does not recognize Greek or Hebrew, but what app really does a halfway decent job with that apart from ABBYY FineReader. It would be unreasonable to expect GoodNotes to turn handwritten Greek or Hebrew into digital text, but one can dream.
You can pinch zoom on the GoodNotes paper and write, but I recently started using the zoom window, which allows me to have a larger writing line, while also letting me see more of the page.
As far as what type of notes I write down, this is my rule: If I look it up for any reason, I write it down. Usually it's vocab notes, sometimes notes from a grammar, and occasionally something more reflective.
There are times when I use Accordance and GoodNotes in split screen. Because of the auto-advance feature of the zoom window, I can write continuously even though I have a relatively small space, half of a horizontal 9.7" screen. You can see an example and more explanation of this feature at the bottom of this page, but check this out, too.
I can also copy and paste right along side my hand writing, and if I don't like the way something looks, I can erase and rewrite it or cut and paste it somewhere else — yes, even the handwriting.
I read at odd times throughout the day. Maybe it's in the thirty minutes I have just before the students come streaming in, or maybe it's while they are taking a quiz. Coffee shop, office, whatever — no matter when and where, I have my notes with me. Being able to share my notes with others is pretty sweet, as well.
GoodNotes and the Apple Pencil work so well together that taking reading notes sometimes feels like art. I can't imagine a better digital notetaking environment.
A couple more pics: