Minimising App Windows Into their Respective Icons On The Dock To Create Less Clutter?
I think you are looking for this feature:

(System Preferences => Dock)



I just tried it on my own system and it when you minimize, it minimizes on the icon. You can click the icon to make the minimized window appear again.

You didn't mention what version of OS X you are on; I'm on Mountain Lion (OS X 10.8.4).