I know I'm super late in response to this, but ...
... I was a really devout take-notes-by-hands person in undergrad. I decided to switch to my laptop when I started vet school. I wanted all my notes with me as time went on.
So far, I have not regretted that decision one bit. It took me a few months to really get comfortable with it, but once you find a few tricks (like PDF Scissors, and the 'set all as background' command in OneNote) it's really super nice. I love that I can quickly search my notes not just for things I wrote, but for things that were in the instructors' pdfs/slides/powerpoints/whatever.
I use OneNote, but any of the common software packages would work... and I've kinda wondered if Evernote Premium would work for this. OneNote is structured with Notebooks as your top level in the hierarchy, with Sections under that and Pages within Sections (Notebooks -> Sections -> Pages). So what I did is create one Notebook for each semester (Y1S1, Y1S2, Y2S1 ... Y4). Then I create a Section for each class in that semester. Then within that class I create a Page for the Syllabus, one Page for each lecture, and whatever other miscellanous Page(s) make sense.
You can arrange Pages in their own hierarchy up to 3 deep, so I often did something like:
Syllabus
Exam 1
Lecture 1
Lecture 2
Exam 2
Lecture 3
Lecture 4
Exam 3
Lecture 5
Lecture 6
.... etc. Just made it easier to organize since you can collapse the sub-pages, so I'd only expand whatever section we were working through, i.e.:
Exam 1
(collapsed)
Exam 2
(collapsed)
Exam 3
Lecture 5
Lecture 6
Yes, I'm an organizational freak. But there are classes with 50-60-70 lectures or so ... it made it nice to keep it easy to navigate and crystal clear what I had to study for any given exam.