Great question. I think that this should be addressed thoroughly, so I'm going to try to make my answer as thorough as possible.
One thing that I do when approaching large projects that I've either inherited or contributing to is automatically generate their sources, UML diagrams, and anything that can ease the various amounts of A.D.D. encountered when learning a new project:)
I believe someone here already mentioned Doxygen, that's a great tool! You should look into it and write a small bash script that will automatically generate sources for the application you're developing in some tree structure you've setup.
One thing that I've haven't seen people mention is BOUML! It's fantastic and free! It automatically generates reverse UML diagrams from existing sources and it supports a variety of languages. I use this as a way to really capture the big picture of what's going on in terms of architecture and design before I start reading code.
If you've got the money to spare, look into Understand for %language-here%. It's absolutely great and has helped me in many ways when inheriting legacy code.
EDIT:
Try out ack (betterthangrep.com), it is a pretty convenient script for searching source trees:)