The legend is that Achilles was invincible in all parts of his body other than his heel (some versions say that he was dipped in a river to gain invincibility, but that his heel was not covered with water). He ended up being killed by a poisonous arrow to his heel and so the phrase "Achilles Heel" is used as a way to reference someone's primary weakness.
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I agree with the answer from @mrcal. The legend of Achilles (including variations) is where every part of his body except for his heel was made immortal.

An injury to a person's Achilles Tendon can be severe, but severing the tendon disconnects the calf muscle from the foot. That separation renders the leg useless for walking. I have heard that the tendon (if snapped from the heel) will recoil up the leg to the knee. The only way to repair it is to reach up the back of the leg and pull it back down to the foot. (It sounds excruciatingly painful...)

In addition, this is often used to described the one key weakness in a plan that can cause the whole plan to fall apart.
Source(s):
http://www.achillestendon.com/Achilles.html; http://www.achillestendon.com/Injuries.html; http://dictionary.babylon.com/Achilles%27_heel

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According to my Cambridge Advanced learning dictionary, Achilles' heel is actually not referring to the tendon, it means a small weakness in someone that causes their downfall.

The origin of this phrase is from Greek mythology: Thetis bathed his son, Achilles in river Styx to make him immortal. But a leaf fell to his heel, leaving the skin untouched by the water. In Trojan War, Paris killed Achilles by shooting his heel, which is now called Achilles tendon.
Source(s):
http://en.wikipedia.org/wiki/Achilles

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All these answers are correct, but the origin is more generic. It refers to a soldier becoming totally disabled with a very minor wound, such as in the heel.
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