I use one note when researching stuff to keep tabs on the various things I find, but to be honest it's really clunky and I don't really like it.
An electronics lab I joined at uni uses a wiki as a daybook, and for projects (rather than research) it works so well. It's it quite as streamlined for some things (like adding screenshots), but it's much easier and logical to read through what you've already done. And you can edit/read from anywhere, whereas one note support on mobile is pretty pants.
Yeah that would be useful sometimes, I use it a lot for keeping tabs on my references and bibliography when i am writing essays. OU at the moment is a real struggle, The reading is very dry and has not inspired me at all. Hopefully next module will be better.
I use the referencing stuff built in to Word to manage... references. I tried End Note once, and another thing that I can't remember the name of, but it seemed far too complicated for my basic needs.