If it's code that I need to understand in intimate detail, I actually trace through the code keeping notes with pen and paper. I complement a simple reading of

If it's code that I need to understand in intimate detail, I actually trace through the code keeping notes with pen and paper. I complement a simple reading of the code with actually exercising the code with test data and a debugger. I go through a few iterations, each time learning a little more about what is important and what can be safely ignored, until I eventually build up a Gliffy diagram of the important parts.