Another tip for a physical notebook: starting from the back, keep a running table of contents referring to notes pages or dates. Log really important stuff, or everything, according to taste.
I make a text file per project.. and remove items as they are completed.. If the notes are more complex than that, typically it goes into the bug tracker (redmine, or similar)
I've tried using Evernote and Dropbox, but could never make it work the way I wanted hence the motivation to work out keeping note in an ordered way in my notebooks.