From the Eclipse download site one can download the installer
File: eclipse-inst-win64.exe
or download ZIP files.
My question is, on Windows systems, does the installer make any entries in Registry?
Eclipse does not use the Windows registry. It uses different approaches (mechanisms) to persist configuration related information.
You can use command line options to gain some level of control when you are unhappy about the defaults that eclipse is using. See http://help.eclipse.org/kepler/index.jsp?topic=/org.eclipse.platform.doc.user/tasks/running_eclipse.htm for example. Doing so can be helpful when installing different versions of eclipse on the same machine.