Scapple is at its most basic a mind-mapping program. I use the program as a quick and easy brain-dump platform to just get things out of my head, but by its simple nature I believe the program could be used by students to take notes and by historical researchers to organize their data and arguments. I have found Scapple to be very useful and worth the $15 purchase.
To download a free trial visit: https://www.literatureandlatte.com/scapple.php