Interesting question.
I would say, in terms of a black-line rule, that the following are always inappropriate:
1) Anything physical. Whether it be throwing, pushing, punching, or whatever, there's no reason to escalate things towards physical violence.
2) Profanity. There are kids around; try to act like something other than a drunken buffoon.
3) Anything racist. Totally unacceptable.
4) Directly harassing fans of other teams. This bothers me. If a Lakers fan wants to go watch the team in Boston, let him do so. There's no reason to get in his face or jeer him, so long as he's respectful. If he's *not* respectful, find an usher.
The other stuff is trickier. I think the fans want to get into the heads of opposing players, and that's why you're going to see chants about steroids, domestic abuse allegations, criminal charges, etc. Those maybe aren't the most tasteful things to chant about, but they serve as a distraction to the opponent. I wouldn't participate in a "rapist" chant if I was at the Garden, because of concerns about children and the questions that raises, but I can at least see why fans do it.