Personally, I love Layers. You can either take a screenshot and have it in one PSD file as different layers, or have the screen layers divided into separate jpgs or bmps on the hard drive. That way, you don't have to clip out anything. You just look for the layer with the window you want, and it's perfect every time.
I always use the PSD option, since Pixelmator can read PSD's.
http://layersapp.com/
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