The Stinger at the end of "Entertaining Father Stone" has the titular character, who never reacted to anything in the entire episode to that point, smile ever so slightly just for being in Father Ted's company.
At the end of "Night of the Nearly Dead", Ted makes Eoin Mac Love thank Mrs. Doyle for the cake and jumper she gave him. This is perhaps the only decent thing any of the protagonists do for Mrs. Doyle in the entire series.
In the episode "Flight of Terror", when their chances of survival are very slim, Ted tells Dougal that he likes him. Even though Dougal hasn't got a clue what he's talking about.
Same episode, when the Monkey Priest reads out his speech, all he can say are his usual grunts and moans. However once he's done he gets the biggest round of applause yet, it's implied in series that everyone can understand him despite his condition and is well liked by everyone.