The largest collection of Isaac Newton's papers has gone digital, committing to open-access posterity the works of one of history's greatest scientist. Among the works shared online by the Cambridge Digital Library are Newton's own annotated copy of Principia Mathematica and the 'Waste Book,' the notebook in which a young Newton worked out the principles of calculus.
I've annotated something about Isaac Newton's Waste Book for calculus before (possibly in Cambridge's Digital Library itself, but just in case, I'm making a note of it here again so it doesn't get lost.
In my own practice, I occasionally use small notebooks to write temporary notes into before transferring them into other digital forms. I generally don't throw them away, but they're essentially waste books in a sense.