I have tried writing things I don’t want to forget, but I didn’t like it much. I have copied short quotes and added sticky notes at important parts, which I liked, but felt possibly not enough. I tried annotating, but it made me feel bad and disrespectful for the book.
When studying or in classes I usually take note of structure, questions, and stuff I find unexpected.
In structure, I just go for quick notes on how one topic flows into another expectedly. Means no surprises and I can probably retrace those steps myself.
Then I note in questions to be asked or researched about specific points. I don't usually note down the answer unless unexpected.
And then, I note the unexpected things, where I think I can't derive myself from the overarching structure. Terminology and specifics usually fall under this category.
If everything is unexpected, well, that's a sign that maybe I'm not ready for that level of content yet. So I'll generally go for more introductory content before I tackle it again.
On a side note, I don't personally annotate books, but lots of researchers do (I'm not a researcher), and actually defend that respecting a book is annotating it thoroughly. So. That's another take on it. :)