I have more "knowledge"(those who saw my intro thread will get it) over TKD than Muay Thai, but the brutality of Muay Thai really shocked me while I was practicing TKD.
The brutality I've seen in UFC, Pride, WEC and HDnet had me going, but I couldn't just forget about TKD.
Taekwondo concentrates on self-defense, focus, and confidence. It has been modernized eversince it was born.
Muay Thai is based off of a more ancient style "Muay Boran" and it's techniques build up the body, and it can easily be used to end a fight quickly and efficiently.
My pick is Muay Thai because it is a "Straight Forward" art and it relies on simple yet extremely effective tactics to get your opponent down.
Taekwondo is still an art that I favour..but Muay Thai is more dominant.