I mainly used a mix of word and annotating readings/slides in pdf format, but it would depend on the subject. I had a couple of subjects where I only used a small A5/A6 notebook because of the way it was taught or the nature of the content (e.g. symbol heavy). OneNote was very popular amongst my friends if it wasn't word + annotating pdfs. Often it would be the ones with touchscreens/tablets and a stylus using OneNote.
Nearing the end of last year, I started using QOwnNotes and see myself using it for my honours year and beyond (alongside annotating pdfs). Free, open-source, highly customisable, and can run entirely isolated on a USB if required. It can use cloud/syncing tools, but I personally prefer vigilant manual backups (which is habit for me anyway). It's definitely not for everyone, though, since it's very markdown based. I did consider Notion which was mentioned above, but it's lack of a true offline/local mode was a bit of a turn off (it has too many features I'd probably never use too). Being able to mass apply tags to separate notes and then search across all of them for a specific tag is very useful for sorting through and grouping literature/ideas. I vaguely think OneNote can do this, but not exactly in the way I wanted it to work.
Past the programs - spend your first year experimenting with note taking methods if you need to. The nature of uni might make it so previous methods you've used in secondary may not be suitable (this was my case!).