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In Snow Leopard, windows can now minimize down into their respective dock icons. But I very rarely minimize a window. Exposé and Spaces are the right way to manage your windows.
And as for having programs open with no windows running, what do you think your system tray is doing? I much prefer the separation of program from window. There are certain programs that run 24/7 on my computer, such as Thunderbird and Firefox, Adium, NetNewsWire (rss). I don't need their windows to be open until I want to activate their windows, but I do want the programs to be running all the time so they can continue to update themselves, or in the case of Firefox, so I don't have to wait for the program to boot up every time I want to open something in my browser.
On Windows, you're up to the mercy of the programmers for each application. Will they include the ability to run in the system tray? Maybe. If not, then you have no choice but to open the program each time.
The Windows 7 taskbar comes much closer to reproducing that kind of functionality with being able to pin programs to the taskbar and interact with them via context menu like you can with the OS X dock. Definitely a smart move.