I've been using different tools through out my studies. Pretty much settled into Emacs now though. It's been amazing and there still so much left to customize.
Right now I'm pretty much just using org roam, org noter and all the regular org features. You can honestly just use org by itself and you'll be fine. There are so many useful features packed into it which all integrate extremely well.
For my personal workflow I've kept it relatively simple
- one file per course
- one file for TODOs
- create files for topics once they become to big (org roam has some useful functions for this)
- if I don't have a place for some information I usually create a new file but you could also work with daily notes
The one thing I definitely do differently to other systems I've used is that I don't shy away from massive files. Org mode does an amazing job structuring them and allowing you to narrow in on the important bits such that the benefits easily outweigh the drawbacks and Emacs has no problem working with these either.
Sieht interessant aus. Für mich persönlich wird es wahrscheinlich emacs bleiben, aber würde mich freuen wenn das eine erfolgreiche Alternative zu notion wird.