I've got a small A6 notebook for this, computers are great, but there's still work to be done in translating the abstract diagram/flowchart/sketch amalgamation that's in my brain to a digital representation.
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.
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.
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.