I use a large format (8x11 inch) notebook and start going through the abstractions file by file, filling up pages with summaries of things. I'll often copy out the major classes with a summary of their methods, and arrows to reflect class relationships. If there's a database involved, understanding what's being stored is usually pretty crucial, so I'll copy out the record definitions and make notes about fields. Call graphs and event diagrams go here, too.
After identifying the important stuff, I read code, and make notes about what the core functions and methods are doing. Here, a very fast global search is your friend, and "where is this declared?" and "who calls this?" are best answered in seconds. A source-base-wide grep works okay, but tools like Visual Assist's global search work better; I want answers fast.
Why use pen and paper? I find that this manual process helps my memory, and I can rapidly flip around in summaries that I've written in my own hand and fill in my understanding quite quickly. Usually, after a week or so I never refer to the notes again, but the initial phase of boosting my short term memory with paper, global searches and "getting my hands to know the code" works pretty well.
Also, I try to get the code running and fix a bug (or add a small feature) and check the change in, day one. I get anxious if I've been in a new code base for more than a few days without doing this.