There are a few ways to release a minimized window from the Dock. You can click on the minimized window in the Dock, of course, or you can Control-click on the owning program’s Dock icon, and choose the minimized window from the list of windows in the pop-up menu. (Minimized windows appear with a diamond next to their name in the pop-up menu.)
Here’s a third method that can be used in a very specific situation in both Mac OS X 10.5 and 10.6. This method is useful when you’ve minimized the last open window of a given application, and would like to free that window from the Dock. While you can use either of the above methods, here’s a keyboard-based alternative (which is my favorite kind of alternative). e–
Press Command-Tab to activate the program switcher, then–holding Command down–press Tab until the program with the minimized window is highlighted. Still holding Command, release Tab and press and hold Option, then release Command. When you release the Command key, the application switcher will vanish, the chosen application will come to the foreground, and–surprise–the minimized window will free itself from the Dock.
If you’ve minimized more than one window, this trick will only release the most-recently-minimized window. It also may not work in all applications, though it handled everything I threw at it during testing. Thanks to Mac OS X Hints contributor les0sx for this bit of keyboard trickery.