I'm in grad school working on an MS in EE and for note taking have found that nothing beats plain white copy paper. It's cheap ($2-3 per ream) and with a 3-hole punch and an inexpensive 1” 3-ring binder is very versatile. I have one binder for each course. I like the 1” binders because I can easily fit 2 or 3 in my bag. I have tabs to divide syllabus and course schedule, notes, handouts, and blank paper. Other tools include a big pink eraser, a Z-Grip 0.5mm mechanical pencil, and Pilot G-2 0.7 mm gel pens in red and blue ink and a G-2 Pro fine point in black ink. With these tools I can quickly capture notes and diagrams. The only things that I type up are homework assignments and lab reports. In my computer, I have files for each class and sub-files for homework, labs, and lecture notes (PowerPoint presentations and PDFs supplied by the professors). With my trusty Moleskine small square notebook to keep track of my deliverables and other stuff I am able to leave my computer put away until I get to the library. As far as software, Open Office fills all of my needs. I have access to Matlab and Cadence through the university. I actually got my undergrad using Notepad on an old 386-DX2.