If you have a lot of papers to keep track of that don't fit well in your book (updated script or score pages, extra dramaturgy packets, etc) I find that an accordion file can be really useful for keeping track of things.
Clear sheet protectors in the front of my book hold things that I am referencing constantly (contact sheets, schedules and calendars, etc) so that they are easy to access and/or grab out of the book quickly. I also know stage managers who have used a clear plastic clipboard for keeping track of papers, with a cast list clipped face down at the back of it (so that it shows through the clipboard for easy reference.)
I print out a copy of rehearsal reports, store them in a section of my book, and look through them each day, highlighting notes that have been taken care of. I find it a good way to see which notes haven't yet been addressed.
I also try and get rid of any paperwork that is out of date or no longer useful as soon as possible. It's so easy for things to accumulate- I keep a recycling container near wherever I'm sitting.