1. Lock the infernal icons so that inexperienced users can't "poof" them
2. Make the dock superficially display icons for every window running whether it is maximized or not.
Is your dock at the bottom of the screen? I've never "poofed" icons from
the dock when it's on the left. I have done that in the sidebar of
Finder windows, but that's easy to fix. It's just another D'Oh moment,
though.
In the top menu, there's almost always a menu for "Window" which lists
the open windows in a program. With many programs and windows open, it
wouldn't help to have them in the Dock since the icons would be too
small to see. Only minimized windows have Dock icons, and only for the
program you're using at the time.
Use Exposé to see or hide all windows.
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