Multiple people have pointed out that calling Epic Mickey's "moral choice" system as "good or evil" is just completely missing the point, because it's not about good or evil in the first place.
And finally, why the hell, after all this time, have anyone NOT mentioned Shin Megami Tensei? The hilarious irony is that it's a JRPG that did mons years before Pokemon, and yet, I think, it's got the best choice system besides Mass Effect, because it's not about good or evil. Hell, there's three main options - "Law", "Neutrality", or "Chaos". All three options are generally depicted as morally ambiguous, Law and Chaos can be either a good thing, or evil, if taken to the extremes.
Law - Also known as 'Order', is associated with civilization, authority, rules, protection, the status quo, tradition, and, when stretched to its most evil extreme, mindless obedience, fascism and xenophobia. When they have powers associated with them, it's often leadership, The Virus, Brainwashing, and the power to bind with rules and oaths.
This side is always associated with God and his subjects. Except, generally, in Shin Megami Tensei (until recently), God is a total jackass, and egotistical one at that. He is the final boss in Shin Megami Tensei II, no matter what side you pick, even the guys on the side of Law know he's gone overboard. However, He's acting the way He does because something is very wrong with the universe, and it's causing Him to act differently beyond His will.
Chaos - associated with change, Tricksters, free will, creativity, individualism, and, to its evil extreme, madness, savagery, solipsism, and selfish overindulgence.
This side is associated with Lucifer and his minions. Though, problem with this, however, it's LUCIFER. On the other hand, it's hard to tell whether Lucifer is actively malicious or if he really does think what he does is for the greater good, because God is an egotistical jackass most of the time.
Neutrality - the idea of a balance between the two. Neutral endings tend to be canon in SMT.
Asides from the ending and what kind of bosses you fight closer to the end, the various sides do have a consequence - certain demons are more likely or less likely to join your party, depending on the alignment you have currently. It's one of the more unique 'moral choice' systems in gaming, if not the first.
And, if that's not enough, SMT3: Nocturne offers several choices, based on certain characters' ideas on how to make the world a much better place, and all of them have their ups and downs, and at the end of the game, a new Earth is created based on that ideal or "Reason". The 'Neutral' choice is to decide to just restore the world back to the way it once was. The "True Demon Ending" is basically siding with Lucifer, deciding to end the cycle of rebirth and genocide of billions of people and go after God himself, and even then, you don't know if you're just a pawn of Lucifer or not.