Minimizing windows to the Dock is one way to keep them hidden yet easily available. That is, they’re easily available unless you also hide the application that owns those windows. When you do that, the minimized windows vanish from the dock. They’re not really gone, obviously—they’re just hidden like the rest of the application.
So how do you get them back? You could switch to the hidden program, which will unhide it, thereby revealing the docked windows. But this is time consuming, especially as hidden applications move to the end of the Command-Tab switcher order. So here are two alternatives.
The first, and easiest, is to click-and-hold on the hidden application’s dock icon. When the contextual menu appears, you’ll see all of that program’s windows listed at the top of the menu. Minimized windows have a gray diamond next to their name; select one of those windows, and it will spring forth from its hidden spot on the Dock.
The second way to get to these hidden windows is harder, but it lets you browse all your hidden windows from every application, without having to click-and-hold on each program in the Dock. To use this method, you’ll need to make sure that you’ve enabled keyboard access to the Dock. To do that, open System Preferences -> Keyboard & Mouse, and go to the Keyboard Shortcuts tab. Look at the Keyboard Navigation section and make sure there’s a check next to either ‘Turn full keyboard access on or off’ or ‘Move focus to the Dock.’
Once that’s done, you can access hidden minimized windows by pressing Control-F3, which then sends all your keyboard input to the Dock. Use the right arrow key to move towards the Dock’s trash can. After you pass your last application icon, keep pressing the right arrow key, and you’ll see that the Dock stops on each of your minimized windows, even though you can’t see an icon form them—all you’ll see is a line of text above the dock with the window’s title. Select the window you want to open, then press Return.
This works in both OS X 10.4 and OS X 10.5, though it’s a little nicer in Leopard—the name of the hidden window appears slightly lower than that of any other items in the Dock, making it clear there’s something different about the currently-selected object.