Re: The Aligorical Aliens!
I agree with R. Star's earlier post about the Trek races not really being anyone in particular. That being said, I think you can read into them what you want, and I've sorta seen the Federation as a whole as the Western powers/NATO, with Earth as America (emerging late into the world/quadrant but quickly becoming the primary power) and the non-human Federation worlds as the various European states (similar in values to Earth/America, but older and more cautious).
In TOS their origins are pretty specific and they played a particular role. They did take on a "life" of their own, though. In past threads on this topic I've put forth the idea that the Vulcans represent the Japanese in some ways. McCoy's line about Vulcan being conquered is part of this.
The boring one, the one with Khan, the one where Spock returns, the one with whales, the dumb one, the last one, the one with Kirk, the one with the Borg, the stupid one, the bad one, the new one, the other one with Khan.