I've been thinking about this in the context of ending choices; Fable II, Deus Ex 1-3, Mass Effect 3, and especially Bastion. I think what I've come around to is that all choices in games are meaningless, and they only have value insofar as they measure the investment you've already made in the game.
Bastion is a good example to illustrate what I mean. Bastion allows you to pick between two endings. Obviously you can watch the one you didn't pick on Youtube or reload and replay or whatever (as you can with any game or any choice--anyone who played ME1 did a second playthrough where they picked the opposite choice at the nuke scene), so there's no actual consequence. However, if you've invested in the characters/setting as you've played the game, you internally have a dilemma to face. Yes, it's about nothing, but if you have even the slightest pang of guilt inside you, then you perceive that the choice impacts your emotional investment so far.
What I'm trying to say is that maybe instead of trying to measure the value of a choice, we should use the choice as a way to measure the way in which we value the game up until that point.
Fable III might be a counter-point, based on the rather significant choice made in the introductory scene.