pycdep is a tool for analyzing and visualizing C/C++ header file dependencies. A script extracts information about your code and dumps it in a Prolog database, which is used to query the dependency graph. It comes with a large number of predefined queries for finding out which files include or depend on which other files, how files depend on another file, circular dependencies, transitively implied dependencies, and design rule checks (limitations on which project can include from which other project). Visualization is supported by dumping graphs to .dot files. It also has the beginnings of a natural language interface.
openPLM is a Web-based Product Lifecycle Management (PLM) application. It provides a configuration management system that manages all kind of files and data as documents in a product structure. It supports documents, parts, BOMs, part-document links, electronic signatures for objects, revision management, check in and check out for all files, plain text search using the Xapian engine, navigation between objects using Graphviz, and user management that allows sponsorship, delegation, and rights. Plug-ins are available for Thunderbird, OpenOffice/LibreOffice, FreeCAD, and Gedit.
Theorem Linker is a program used to visualize references between theorems in a paper written using LaTeX. Using a .tex document (and a .aux file, created by the LaTeX compiler), Theorem Linker will search through a paper, find theorems, and find references to other theorems within a theorem's "proof". It will then create a digraph in a .dot file (to be opened with programs such as Graphviz or OmniGraffle) that will display each theorem as a node, with directed edges to describe the relations between the theorems. A path highlighted in red describes the longest path in the graph. Theorem Linker will also create folders containing graphs to individually show relations of each theorem in a paper.
code2flow is an experimental script which sweeps through your project source code, looking for function definitions, then does another sweep, looking for where those functions are called. It connects the dots and presents you with a flowchart estimating the functional structure of your program. It is especially useful for untangling spaghetti code and getting new developers up to speed. code2flow is experimental and meant to provide a rough overview of the structure of simple projects. Source code which is just a little esoteric will break this. Even with normal code, there are many known limitations and many outright bugs.