"The Drumhead" comes to mind.More "broken ground", I don't often recall when TOS was doing personal attacks against LBJ or Nixon. The show did comment on Vietnam, etc, etc, etc... TNG did its share of commentary as well, but how often did they go after current political figures as opposed to mere situations, either real or theoretical based off of real events?
Also, "The High Ground" which is basically an allegory for the Troubles in Ireland and/or Israel vs. Palestine. Bajor vs. Cardassia has similar undertones but is far less specific.
STID had this line from Spock: "There is no Starfleet regulation that condemns a man to death without a trial, something I believe you and the Admiral are forgetting," which is a DIRECT and very appropriate shot at Obama's drone-strike program. And Admiral Marcus' agenda, plus his rant at the end of the film, echo the whole "War on Terror" concept pretty directly.
Hell, even ENT had the Xindi Probe as a thinly veiled 9/11 parable.
DS9 had Kai Wynn leading a boycott of Keiko's school because she dared to call the Prophets "Wormhole Aliens" instead of admitting they were divine beings and encouraging her kids to worship them. And in various times, the Bajoran Resistance came up as a plot point where they were indirectly compared to Hezbollah and had to come to terms with the implications of their terrorist past while also struggling to become something more.