This is a tough one, But I'm going to go with Ben's fate in Episode 4.
I love how on the surface, it's one of the most basic A or B choices in the game; save this guy or drop him to his death. Very Paragon/Renegade esque choice.
But, add context, and it becomes so much more complex. This is a guy who has endangered the group on multiple occasions, contributed virtually nothing, put the young 8 year old girl (who most players are VIOLENTLY protective of) in immediate danger to save his own ass, and is basically responsible for at least 60% of everything that goes wrong. All the while acting incredibly angsty towards you.
On the other hand, he really does mean well, he's aware of his role as a burden and potential danger and he wants to do everything in his power to make it right. To the point where he's willing to take his own life so that the rest of the group can make it that little bit further. Plus Clem likes him, and we all like Clem.
You could drop him, save the group a lot of potential trouble, and (if your the spiteful sort) get a little bit of payback for endangering Clem. OR you could save him, a decision which Ben himself will disagree with, and stand against the dogmatic, survivalist lifestyle that Crawford personifies.
Practically, it's a really lopsided choice. With nothing good really coming from saving his life. All you get is that warm fuzzy feeling of "I did right."
But that's kind of the point, it's a question of pragmatism vs humanity.
It's surprisingly deep, and the reason it's my favourite is that it challenged my beliefs the most out of all the choices. Being the cynical, callous asshole that I am, (and hating Ben for being useless, as well as the least interesting character in the game) I totally expected to drop him when the choice inevitably came. But I didn't, for many reasons. I didn't want to wind up like Crawford, or to a lesser degree, I didn't want to start thinking like Kenny. I knew that Clem would somehow find out, and it would create a considerable rift between us. I also think that Ben redeemed himself in those last moments, proving to me that despite his ordinary nature, he was still willing to do what he could for the good of the group, to the point of his own death, and to me that invoked the right to a second chance. From that point on, I was Pro-Ben
...and then Episode 5 happened.
Ultimately, I discovered that I'm a much nicer guy than I thought I was. In fact, as far as the argument is concerned, I'm about as for humanity as it gets. The survivalist mentality has common sense on its side, but that's all its got. The worst part is, I can't even defend my stance, there's no real way to explain why humanity is the stronger side, it just...I don't know, 'is.'
Also hi all, I'm new here. If you couldn't tell, I have a tendency to ramble and digress like a drug-addled moron; enjoy that.