Enzyme is an architecture for creating user-searching-user applications. Right now, it is primarily useful as a resume create/search and HR management system. However, it's potential uses are wide-ranging, and it offers PHP developers an alternative to relying on simple "keyword" searching systems.
Jmol is a Free, Open Source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it on a daily basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.
Todolist.php is a set of PHP scripts that creates a Web-based list of things todo. Items can be added and removed, and are sorted by an assigned priority. It is also possible to assign special tasks to another person and to specify a due date. Tasks are organized in projects. Todolist.php supports several languages.