Although it is not specified exactly in the question I shall assume you are using ADS 2009U1 or earlier. ADS 2011 uses workspaces and not projects.
For a project to be recognized by ADS there are three essential components. There must be a networks and data directories inside the project folder. The project folder name can be anything, it does not need to have the _prj ending, but these two directories must exist with the correct name. Also the must be a file called de_sim.cfg in the project folder.
If any of these three pieces is missing then the error message about "Not a Project Directory" will appear if you attempt to open that project.
Incidently, for ADS 2011 the requirements are the same in repect to the data directory and de_sim.cfg file. However, instead of the networks folder being a requirement it is the lib.defs file that is needed.