I have moved all my research and education into an electronic format. Microsoft OneNote is my main tool at the moment. It is the most valuable software to me, thanks to inking that my Surface enables.
I have all my notes in OneNote. All research material is there, including both plans and results. And also all my course material is in OneNote.
In education I use OneNote Class Notebook. With that I can share the material with the students. And they can then also share their material with each others and me. I like OneNote since it supports all formats I need. And in a free form – A4 pages are too old-fashioned to me.