Star Trek is a horrible, awful show for libertarianism, but I love it. I can't help but wonder what species embodies us most though, it's hard. Right away the big ones are thrown out, humans, Vulcans, Klingons, Romulan, Cardassian, Borg. The center of each society is a powerful, worldwide government. There are elements of the humans, Vulcans and Klingons that may seem attractive (like the Klngons need to hold even their leaders accountable to the law by killing them in combat), I think they aren't on a whole very freedom loving.
The obvious choice seems to be Ferengi, but they have a pretty powerful regulatiory organization, and they are extremely misogynist.