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)
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'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.
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[ 4.8 ms ] story [ 25.9 ms ] threadI use a text editor along side with the IDE so I can add notes as I code;the same way as physical notebook but I can paste code bits in there