I bought a Surface Pro 3 to use OneNote, and I'm quite happy with it. I think the best part is that instead of having to carry both a laptop and notebooks or paper sheets for taking notes, now I just carry a light laptop. My back is much happier since I stopped carrying around hundreds of sheets (easily weighting more than a conventional laptop) in my backpack. It's not a cheap solution, though: I spent 700€ for the SP3, plus 120€ for the keyboard (not really necessary for taking notes), and this was for the lowest-end model at a time when the SP4 was already out. Think of all the paper you can buy with that...
I take my notes just like I did on paper, which means I hardly use the keyboard. So I just mix handwritten text and math and sketches like on paper. One major advantage, especially for people who, like me, aren't very good at drawing, is that you can delete each line as many times as you want until it comes right. All of a sudden, I can figure out what I've drawn :)
I zoom in for drawing details, and resize stuff when I need to make something bigger e.g. to make the details more visible. Once in a while I insert snippets from exercise sheets and the like so I can draw on them, or fill out tables, etc.
I can't imagine myself figuring out the LaTeX representation for formulas or whatever as I try to copy stuff from a whiteboard. And I'm not going to be solving exercises in LaTeX, either. For me, it was either this or paper; sometimes I need to use paper (for taking exams, if not for anything else) and I don't find it strange at all.
I have handwriting recognition disabled as it doesn't tend to play very well with math formulas and the like, which means I can't use search, but then again paper doesn't offer full-text search either. Having recognition disabled has the added bonus of improving battery life.
I tend to organize my notes as I write them. I rarely reorganize stuff later - it's been like this since I started taking notes on paper. It never takes too long to find what I'm looking for so I'm probably doing this right...
When I need to share stuff with other people I just export the pages from OneNote. But it's still hard to send handwritten stuff through e.g. Skype.
You see, I like this setup so much that I'm willing to put up with Windows even though I don't like it very much. I'm getting a degree in computer engineering and as I move on from math and physics courses I believe I'll stop needing to write so much math, to a point where plain-text files will suffice and I can go back to my beloved Linux shell. But then I can't mix sketches with text...
By the way, when I say OneNote I mean the full Office version, not the Windows Store "app" version, which is still crap. Both are free. However, I think the reason for the success of this method is not so much the software, but the digitizer pen...