Paper rocks. I really like its battery life, negligible boot-up time, customisability, interoperability and extensive unicode support.
The main downsides are poor search, scriptability/automation, and backup support.
The number of hours I have spent trying to find an alternative note taking system to paper is rather more than I like. Unfortunately search sucks, they tend to get lost and I have horrible handwriting.
Paper beats silicon.
The computer is a gateway to a billion distractions, my most productive days are the ones where I manage to write down the most on paper. The physical act of writing helps memory, and it works everywhere.
Physically checking checkboxes is also fun, as is crossing out plans that become irrelevant during the day.
A picture tells a a thousand words, there's pages where I tried redesigning a scene graph implementation, it'd take hours to transcribe the knowledge that I gleaned from those (roughly drawn) images into words.