Can an app window be minimized by clicking its Dock Icon? Something that bothers me as Windows user on OS X is that I can't minimize an app window by clicking the dock icon of the application. Is there a hidden setting for enabling this behavior or a utility that someone could recommend?
You can hide an active application by option-clicking (alt-clicking) its icon in the dock. You can also hide the active window and open another window by alt-clicking whatever application you want to open in the dock.

But I agree with you that it would be more symmetrical to be able to click to minimize all the open windows in an application. I am a long-time PC user and this is one area where PCs got it right. That and combining closing and quitting (and the related window management issue).