Check this site for a survey of source code comprehension tools (these show flow and/or relationships of function within the program in a graphical and/or text manner). Both free and commercial products are listed.
OpenGrok is a fast and usable source code search and cross reference engine. It helps you search, cross-reference and navigate your source tree. It can understand various program file formats and version control histories like SCCS, RCS, CVS and Subve...
Cxref is a C source code cross referencing and documenting program for UNIX, written by Andrew M. Bishop. Cxref makes both html and latex style document.