For most type of projects in Eclipse, the source files and most of the project information is stored in the workspace directory, under a subdirectory with the project name. However, special types of projects like those created from a Makefile are not stored in the workspace. So obviously, Eclipse is storing the list of projects in the workspace and their information in some other location.
This information can be found in the workspace directory under
.metadata/.plugins/org.eclipse.core.resources/projects. Information about each of the projects in the workspace is stored here under its own subdirectory.
Tried with: Eclipse 3.7.2 and Ubuntu 12.04 LTS