To me there are a few TOS episodes. Omega Glory comes to mind. The savage "Yangs" (who are white) that love freedom and the "Kohms" (of Asian descent) are oppressed. Great racist undertones and symbolism Roddenberry (as I think he wrote this one).
There are some others like Patterns of Force that seem to play as a joke on the Nazi manifesto. Others were Kirk "frees" a society by destroying their leader (the Apple for example). The message in the latter seems to be "to be happy one must be free" overlooking the fact that what humans consider "happy" or "free" is not what other races or aliens might agree.