Using Eclipse as your build system for production code seems like a bad idea in general. I think it's a great IDE and have used it extensively for both Java and C++ projects, but for a build system I firmly believe that Ant, make, and other dedicated build utilities are the way to go.
There are several reasons for this:
Dedicated build utilities offer the very flexibility you are looking for in generating multiple executable targets.
Ant and make support most conceivable arbitrary build process chains (though not quite all).
A dedicated build utility is likely to offer greater stability and backward-compatibility for build description file formats than an IDE tool like Eclipse. Also, I'm pretty sure that Eclipse's internal build feature is dependent on the ".project" file description, and the latter's format is probably not as stable as the build description format for either Ant or make.
General-purpose, basic build utilities are usually command-line-based, which makes it easy to integrate them with more sophisticated, higher-level build utilities for automated build management like Pulse, CruiseControl, etc.
The need that is motivating your question is telling you that it's time to make the switch to a better build tool.