Hi everyone, long time lurker here.
A few years ago, I wanted to switch to Linux as my primary OS, but after finding alternatives to almost every other proprietary app I used without native support, I couldn't find anything that accurately replicated OneNote's structure. I'm not a fan of the fact that the web version of OneNote prevents you from saving notebooks locally (and I also just prefer native software), and although wiki editors like Zim and similar programs are very well made and great for subdividing your workspace like a notebook, they lack OneNote's distinctive "click anywhere to type" feature.
After learning the basics of QT and a lot more development time than I initially planned for, I've been using my program, Spiral, as my primary note-taking app for college since last fall, and I thought I'd share it here in case anyone else happens to be looking for this type of program.
I should note a few things, though.
First and foremost, I don't personally use handwriting tools, so, unfortunately, if you require that in a OneNote alternative, you'll probably want to look elsewhere. That's not to say handwriting support will never be added, just that it's not on my radar right now.
Second, although I haven't lost any data while using Spiral, I would strongly advise that you make frequent backups just in case since the amount of testing I've done is probably not exhaustive of everything that could go wrong in a program like this. (Personally, I use abraunegg's OneDrive client for Linux, so OneDrive's revision history is always there for me in case I need it.)
Since this is mainly just something I've worked on in my free time (and since I'm still relatively new to this type of software development), I really only focused on implementing the features I needed from OneNote, so if there are any super important features I missed, I welcome any and all feedback.
Anyway, if my disclaimers haven't scared you away and you're craving this type of program for Linux as much as I was a year and a half ago, you can download Spiral at http://spiral.augustin.tech.