Like others have mentioned, I still do handwriting in a notebook, mainly because it's easier to sketch a diagram with a pen and paper than it is to do it digitally.

Pros of handwriting/pen+paper:

    - Extremely high "resolution" (can fit a lot of information in a small space)
    - Flexibility
    - Direct input: tools rarely "get in the way"

Cons of handwriting/pen + paper:

    - Editing is cumbersome
    - Storage/retrieval is annoying (no search!)
    - Sharing/collaboration is not as good as digital

I'm still dreaming of something like the Microsoft Courier Concept [0]. We've gotten a lot closer since the concept came out (e.g., the MS Surface), but I think we're still not quite at the point where a digital notebook can feel just like paper + pen.

[0]: https://www.youtube.com/watch?v=UmIgNfp-MdI