Barring running the code... I prefer to start with a quick scan through the foundation code. What does the math library look like? How about the file and network I/O? Next, locate the top-level main loop, then the top-level Update Everything/Render Everything functions. At that point, you'll understand the general theme of the code and you'll have spotted lots of interesting avenues to explore.
EXTRACT_ALL
Also, different parts of the code are covered by many different licenses and the copyright on them belongs to many different people, so it is important to be very explicit about everything.
When it's an OSS project owned and operated by a small group of people, there's little motivation to worry about this stuff. Also when you choose a license like the MIT one which basically says "I really don't give a fuck what you do unless you sue me," you have a lot less incentive to plaster it over everything, because you're one step away from being in the public domain anyway.
When you're releasing the doom3 code, things are very different.
What I meant (probably poorly phrased) is that for readability for personal study (like gcv was asking about), I think it's worth stripping huge license preambles from source files. There's obviously good legal reason for them being present to start with.