Hayta-UML is a Web2.0 UML tool, that allows users to draw UML diagrams. A core design decision is to have a native version-control inside the application.
PHP Project Navigator is a web based source browser for PHP. Its parser uses the same YACC grammar as the Zend Engine 2 so it recognizes PHP 5 syntax and inline documentation blocks. Symbols are stored in a database which is queried via a web based GUI
Recon-Calc is a source code feature location tool based on the Software Reconnaissance technique. It allows you to name features of your system and then, based on coverage profiles gathered, you can find where they are implemented in the source code.
DoxyChange is an extension of Doxygen which provides a mechanism to display changes in SVG/HTML/UML format between two revisions of a given software system.