Surface Pro (or any windows tablet with a wacom-like stylus) with Onenote addresses all of these issues.

Especially since you can easily screengrab portions of the screen (e.g., a relevant theorem from a pdf) and 'print' anything to any onenote page, it's really clean and easy to get all relevant content in one place. It also makes your handwriting and printouts searchable. I also really like using the webcam to take pictures of whiteboards/lecture slides to annotate on top of (really helpful for 'old school' classes or Professors that don't share their slides).