I am neither student or graduate, but know Windows outliners.
Use Google to find the Web sites:
These are NOT in preferential order.
One-window outliners: NoteMap, MaxThink, Inspiration 7.5
Tree-based outliners/Personal Information Managers: There are hundreds of them:
Free: Keynote, TreePad Lite, Golden Section Notes
$$: Jot Plus, MyBase (teriffic for saving Web pages), TreePad
Another product worth considering: Zoot. (zootsoftware.com) This is strictly text with little or no formatting and no graphics. It has a steep learning curve. But you can set up rules to link notes to words, concepts, etc and Zoot will automatically use the rules to link the notes for you.
Steve Cohen, Ph.D.