Why does Eclipse Java Package Explorer show question mark on some classes?

It means the class is not yet added to the repository.

If your project was checked-out (most probably a CVS project) and you added a new class file, it will have the ? icon.

For other CVS Label Decorations, check http://help.eclipse.org/help33/index.jsp?topic=/org.eclipse.platform.doc.user/reference/ref-cvs-decorations.htm

With some version-control plug-ins, it means that the local file has not yet been shared with the version-control repository. (In my install, this includes plug-ins for CVS and git, but not Perforce.)

You can sometimes see a list of these decorations in the plug-in's preferences under Team/X/Label Decorations, where X describes the version-control system.

For example, for CVS, the list looks like this:

These adornments are added to the object icons provided by Eclipse. For example, here's a table of icons for the Java development environment.