If your product-based Eclipse PDE Headless Build seems to work just fine and creates some archives with files and executables inside, you might still experience one ugly problem:
Unable to acquire application service. Ensure that the org.eclipse.core.runtime bundle is resolved and started (see config.ini)
This message will appear in the error log, brought to you by a very plain dialog box. You can solve this problem by editing the product definition file. In the Configurationsection, add the plug-in org.eclipse.core.runtime to the list. Then enable Auto-Start and set the Start Level to 2. Since the default start level of OSGi bundles is 4, this will ensure that this plug-in is loaded before the others.