Before Mac OS X Lion, minimized windows were sent to the right-side of the dock. This works well if there are only a few icons, but can grow unwieldy if you add too many.

Lion’s ability to send these minimized window into their respective application dock icons is a good choice. I find that I’m actually minimizing more windows than I ever did before just because my dock doesn’t get cluttered.

The option is in System Preference > Dock.