I was using Post-Its to mark pages and add comments, but I stopped after reading some warnings about the glue damaging pages:

https://siarchives.si.edu/blog/post-it-or-not-post-it

http://libraries.ucsd.edu/preservation/postits.html

It's not clear from these articles how soon damage becomes apparent; I haven't noticed any yet in books which had Post-Its. It may not matter if you don't intend your books to have archival value.

I've tried Book Darts for marking pages, and they can also be used like paper clips to hold notes. I write short notes in pencil, but try to avoid dark leads which make marks hard to erase.