All the Murgatroyds from Ruddigore, but Sir Despard in particular, who boasts of doing good deeds every day after committing the obligatory daily crime.
1776: The main "antagonists" in the play (John Dickinson and Edward Rutledge) are established as being fundamentally good men with different ideas as to what is best for America. The only thing about them that's really villainous is that Rutledge is protecting slavery—but, as he himself points out, Thomas Jefferson is himself a slaveholder.
Fiddler on the Roof: The Russian Constable is portrayed as a pretty decent man who has earned Tevye's respect, and Tevye has earned his. When he is ordered to perform a pogrom, he is clearly disapproving of the idea, but goes through with it because he knows that if he refuses, he will be replaced by someone else who will very likely be much worse toward the Jews than he is. He is shown limiting the destruction to some extent, and prevents any Jews from coming to bodily harm during it, and also warns Tevye about it beforehand. He is also shown to be both angry and sad at the order to evict the Jews from the town, but, again, it isn't within his power to defy that order.