Thank you heaps for a great rant! I'm currently attempting a pair of anti-heroes as my main characters and this has been a great help!
As for common justifications for objectionable actions, I'd have to add the good ol' "They're not people" or "They are not like us" argument that generally leads to the conclusion that morals can be suspended in the case of others. For example, if a culture considers murder wrong, they may chose to see their enemies as "not people" for whatever reason, thus making it ok to kill them. This is used often in fantasy (usually along the lines of "evil henchmen aren't people, so they're fine to kill) but strangely enough it is never seen as questionable.
I want to use religion as a justification too. My morally questionable character worships one of the dark gods and lives in a world where it's pretty well known that you get reborn after you die. In his religion it's not considered a bad thing to kill someone weak, better for them to die and be reborn as someone stronger.