I use an app called Drawboard for annotating PDFs. It's great. Hand written notes, highlighting, multiple colors, etc.I'm in a similar situation as a college student (computer science and web/graphic design). I too have an rMBP which is my main machine but am still very interested in the SP3, specifically for the form factor, OneNote, and stylus integration, not to mention full Windows. It would be nice to be able to bring the SP3 back and forth from campus instead of my 15in rMBP. Anyways...
Does anybody have experience with digital textbooks and OneNote? I think that will be the deciding factor for me. I have PDF versions of most of my textbooks and would love to be able to just carry the SP3 instead of all the textbooks. How is annotation? Is it really worth the price tag? I would really appreciate all feedback but specifically from college students.
The only thing I suggest if you're going to go all-digital for notes is to have a serious backup plan. I save everything to OneDrive (in case my device is stolen, is destroyed or fails) -- and to the SP3 so I can access when off-line, and I also have everything auto-backed up when at home via Windows File History to a networked hard drive in case my online copies become corrupted or my account gets hosed somehow (and since any potential errors may get copied down from the cloud to my device itself before I discover it).
Always better safe than sorry.