I have a webapp containing some Java-classes within some packages. However within Package-Explorer only the names of the packages are listed, but I cannot get the classes within them. Thus the icon for the package stays empty meaning there is no content within the package.
When I manually drag a class from the WinExplorer into the Package-Explorer I get a warning that the class is already contained in the package. Having said this the package is not empty, however I cannot get any of its classes.

Check Project-->Properties-->Java Build Path-->Sources tab.
Make sure that "Included" is properly set (Usually to "All").
Also check that the "Filter" (little triangle icon) is not hiding the required code sources.
You can also try to "New-->Java Project" than use the existing sources.