1) For teaching about liberation theology: the clip from The Life of Brian when the folks in the back get into an altercation while Jesus delivers the Sermon on the Mount, saying "blessed are the peacemakers." When I lived in a base community in El Salvador, the Sermon on the Mount was part of daily ritual, and I find sharing it with students is one of the best ways to explain the parts of Christianity that liberation theology emphasizes. Bonus use for the clip: since the crowd in the back mishears Jesus as saying "blessed are the cheesemakers," you can tell the students about the cheese-making Quakers who moved to Costa Rica after that country abolished its army.
4) For teaching about the Spanish Inquisition: the Spanish Inquisition clips from the Flying Circus, of course. I think that the "torture" scene where the lady is pummeled with soft pillows is probably the most useful, because it makes it possible to introduce the idea of the Black Legend of the Spanish Inquisition, and all of the ways that we now know that it was exaggerated for English consumption. The very fact that the Pythons are doing sketches about the Spanish Inquisition says something about their own educations, although naturally they subvert convention in a way that may be pedagogically useful. Of course the Inquisition was more than soft pillows, but this may help to both introduce and dislodge the idea of a "totalitarian" Inquisition.
5) For teaching about anarchism: the anarcho-syndicalist peasant from the Holy Grail. Anarchism was a major political ideology, especially in fin-de-siecle Argentina (but also in Mexico and elsewhere). With Occupy Wall Street and the like, students today may be somewhat more familiar with anarchist ideas than they were even five years ago. But it is important to reinforce the notion that anarchism is not the same thing as chaos, nor of individualism. The anarcho-syndicalist peasant explaining commune rules can get that conversation started (though should decisions be by consensus?) Apropos of nothing, the peasant is Eric Idle when he is walking but Michael Palin once he is down the hill.
And two general-purpose clips that can help with classroom management:
1) The argument clinic, of course. "But I came here for an argument." "Oh, this is abuse!" A poor model for classroom conversation and debate, but a dead ringer for arguments online.
2) For getting students to relax before an exam: Karl Marx answers questions about football. Just promise them that you won't do this sort of thing to them.