Just enable DeskPins from the System Tray or its hotkey and click the window you want to keep on top. You can pin as many windows as you like, and they'll stay visible no matter what other windows you have open. Click the pin symbol in the title bar to unpin a window. It's that simple.
The program is also quite customizable; you can change the color of the pins, change the hotkey, and even set up auto-pinning for your favorite programs. DeskPins is free and one of those little gens that makes sitting in front of a computer all day that much more tolerable.
While you're customizing your desktop, you might want to check out Expose-like window switching, a utility that prevents accidental window closures, and MaxTo, which lets you specify handy zones for arranging your commonly used windows.