I've tried for very long to find a good electronic solution. Up to and including writing my own wiki with various extensions customised to my diting style, and hunting around for every note taking app under the sun.
The problem, I find, is that nothing beats the flexibility of being able to take out multiple sheets of paper and move them around, annotate them, put them back in. It creates a flexibility in workflow no tool I've tried have managed to match.
The physical presence of the paper also makes it much easier to avoid forgetting a page exists.
I'm not happy with it, but I keep coming back to it after each desperate attempt at making something else work better.