The internet certainly tends to bring out the gullible side in otherwise perceptive people, doesn't it? I've heard that story a dozen times, but it's far from the silliest going around. I can't really go into the details of one particular e-mail tale that many folks have asked me about, but let's just say that any word origin story you may have received lately about manure getting wet while being transported by ship is absolute hogwash.
Onward. The story you received, which claims that portrait painters used to charge by the amount of the subject they included in the painting (i.e., more for the full figure, less for just the head and shoulders) is utter bunk.
The phrase "cost an arm and a leg," meaning to cost a great deal or an exorbitant amount, is simply a hyperbolic figure of speech comparing the cost of something to the grievous loss of two important limbs. There isn't really any "story" behind the phrase, other than the desire of whoever came up with the metaphor to impress the listener with the outrageous price of something. Unfortunately, as is often the case, we have no way of knowing exactly who coined the phrase, although it hasn't been around as long as you might think. Surprisingly, the earliest known use of "cost an arm and a leg" in print dates back only to 1956, in Billie Holiday's autobiography "Lady Sings the Blues," in which she writes "Finally she found someone who sold her some stuff for an arm and a leg." It is unlikely that Billie Holiday herself coined the phrase, but she may well have popularized it with her book.
If I had to guess at the inspiration for "cost and arm and a leg," I'd say that it was probably an outgrowth of the older phrase "I'd give my right arm for," meaning that the speaker would be willing to make a great sacrifice to obtain or do something, which dates back to the mid-19th century. "An arm and a leg" may simply have arisen as an attempt to top that already grisly level of sacrifice.
This is a pretty good site for those who might be interested.
http://www.word-detective.com/index.html