Use Doxygen. It creates an easily browseable cross-reference of the code base in HTML. And it can also create dependency/class diagrams (if the code is OOP).
The code does not need to have specially formatted comments. Although it does help, Doxygen is smart enough to parse the code and figure stuff out on its own. What I like the most is the ability to click on any function name, variable, class etc. and instantly jump to place where it is declared, defined and show list of all places where it is used. I used Doxygen in the past to chew on some rather large code bases (PHP source code, for example) and it saved me a lot of time.
You can also set up Eclipse CDT and import all source files into a project and get a similar code browser. Although, some stuff like function/class index are not available in that case.