First, put zod and a perfect skull in your cube, the go to the secret cow level...
Sorry. Got distracted for a moment. What you do is right click the shortcut to D2 and select "Properties" at the bottom of the list. Next, where it states "Target:" go to the very end and add -w (outside the quotes). When you double click this specific icon, it will open in a 800 x 600 window size. When you play the game itself, it runs under the 640 x 480 size, unless you specify otherwise with the newer patches.
If all you need to do is minimize it, though, you can just press the Windows button if you have one, or press alt+tab.