What is the best solution to build several CDT C++ projects from the command line? The projects have references and so it is not possible to just build single projects.
Pre CDT 6 you could use the JDT's AptBuilder (included with classic Eclipse, for example).
This lets you build an already configured workspace. So you: checkout your source, configure a workspace which points to the checked-out projects. Your automated build scripts can then update the checkouts and run the AptBuilder without needing to start the GUI.