When composing a new message in Mail with one of the stock stationery templates, several of them allow a few choices in appearance. For instance, when the Daisies stationery is applied from the Birthday group, if you click in the window, the color of the background changes from pink to orange to green. There are a few other stationary selections that allow this as well.[robg adds: The only other customizable stationery I found in a quick test was the Bamboo design in the Photos section. Personally, I won't be using stationery, but for those who will, well, you might be able to customize its appearance at least a little bit.]

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