If you need quick access to a particular minimized window, and the application is hidden (meaning that the minimized window is also hidden), Full Keyboard Access provides a method of selecting that window. When you bring focus on the Dock, it gives access to hidden minimized windows by moving the selection between two of the icons when you cycle between the icons in the Documents section of the Dock.
[Editor's note: This is a very useful trick! You'll need to enable Full Keyboard Access in the System Prefs -> Keyboard panel, and then activate the dock using the chosen shortcut (Control-F3 in my case). Once active, use the arrow keys to get to the right side of the dock, and you'll notice that the name of the hidden window(s) appears as you move between two visible icons (the hidden icon will not show, but the name of the window will). If you hide applications a lot, this is a great way to get their minimized windows back without having to first switch to the application...]
Mac OS X Hints
http://hints.macworld.com/article.php?story=20021122053224822