Warning: possible spoilers throughout (mostly about X3)
That was one of the best scenes from all 3 movies. The Last Stand ties back to this scene from X1, where some mutant (Callisto) asks Magneto where his mark is (referring a mark that identifies you as a mutant), he pulls up his sleeve showing his id number the Nazi's gave him and he says, "I have been marked once, my dear and let me assure you, no needle shall ever touch my skin again."
Although I'm pretty sure the persecution of mutants was nowhere near that of the Jews (the lack of death camps or even concentration camps in general is evidence), it does make a pretty good impact. It also shows how fairly fanatical Magneto is, still living in the past to some degree. His mutant vs. human crusade seems to be him wanting to avenge the wrongs from his past rather than correct the errors of the present/future.
Of course, at the same time his crusade would almost help to redeem mutants in general. In his campaign in The Last Stand, the X-Men stand up against overwhelming odds as the only defense the humans have a chance with, even though they defend that which aims to get rid of their kind...a pretty powerful statement.