Or you could keep scores of different consequences of your actions without actually having to have a branching choose-your-own-adventure. Sorta like RPG stats but not of your own character but how you have been dealing with things.
Like the reputation system in New Vegas, or the relationship thing in Alpha Protocol, except you track a lot of more arbitrary things than just how much people respect you. At some point these get evaluated at certain branching points, at the ending "slides", whatever. Even if some later converge, they will still affect how hard some puzzles get later if you use the easy way at the beginning.
EDIT: Actual point & click example. I think it was Kings Quest 4 (I'm not sure, could be confusing with another game), there were a couple places were you had to get rid of some animal to access certain place (different creatures). You could like, throw a rock at one, with no immediate consequence. Or you could use a less aggressive way. But later to get past a different challenge, the game remembered if you were mean to one of these beasties and didn't let you thru. (in this case it rendered the game unwinnable I believe, but this wouldn't need to be so extreme)