I quite liked the paragon/renegade choices and interrupts in Mass Effect 2 and 3. In general games don't get the whole alignment thing right.
General RPG scenario:
NPC asks player for help. Player options are: 1) Help like a knight in shining armour or 2) reject quest because you don't help people / kill everything in 10km radius / do quest then backstab
One of my favourite RPGs was Baldurs Gate 2 but playing an evil character there was just silly. Either you turn every area into a ghost town or you skip/cut short half the game.
Mass Effect took the dialogue options of say blue thing / say red thing and turned it into a rather interesting storytelling mechanic. Like saving / killing the rachni queen.
