Esoteric Happy Ending: Given what ended up happening to the mutineers on Pitcairn in the long run...
Moment of Awesome: Bligh successfully navigating a voyage of over 36,000 miles to Timor with scant provisions. Asshole or not, that's a magnificent feat.
Moral Event Horizon: We all know the film's Bligh is a Jerkass, but his ordering the ill surgeon to be dragged out with him dying as a result really crosses the line. Even Bligh seems to realize he went too far.
Unintentionally Unsympathetic: Christian can come off as this for sending men who were loyal to their captain to what would have been a lingering death if they failed. While Bligh was something of an Asshole Victim, his men didn't deserve the suffering they went through.