I’ve been using Word the first three years of college but I bought a license for NoteBook by CircusPonies last semester and really like it. You have a virtual NoteBook with dividers for each class you are taking and can take your notes in there but can also attach your lecture slides and digital reading materials to it (for pdfs it will show a thumbnail of the first page and when you click it, the pdf automatically gets opened in your pdf-viewer od choice). Today I even saw that it works with Skim (the pdf-viewer) so that when you highlight something in Skim you can automatically copy that to NoteBook and make some annotations to what you have highlighted.

You can also highlight things in NoteBook and it has the ability to export what you have written in many different formats (including Word docs).

I’d definitely give it a test spin. It has a very clean interface but at the same time it has tons of features you can use.