Despite the obvious Fridge Logic, the baby Nidoqueen are so cute! Of course their parents are supposed to be super clones so...
It's not as prominent as some of the other examples, but Meowth bonding with Mewtwo's group and ultimately deciding to help them unselfishly just for the sake of it - something which happens often with the trio of villains in the movies. Because of it, at the end the three have no intentions of taking advantage of Mewtwo and company at all, and everyone trusts them to never to reveal to their boss what transpired despite the hefty reward they would get for doing so.
Meowth: It's only natural to wonder about who and where you came from and someday these little ones are gonna want some answers. Only there won't be any, not if you make everybody forget! So what if their parents were clones? They're all living creatures. They deserve to live, and they deserve to know about themselves as much as you, or me, or anybody does! That's what we think.
Meowth Clone: (meows in agreement)
Ash: I think we should remember too. Meowth is right.
Brock: And just forgetting things doesn't change the fact that they happened.
Misty: Don't you think everybody deserves to know who they are, and where they came from?
Mewtwo: ...Yes, they deserve to remember.
Ash's speech to Mewtwo about helping someone in need just for the sake of it.
Mewtwo: Why, why are you helping me?
Ash: Well for one thing, you saved my Pikachu. That's a good reason.
Mewtwo: The only one?
Ash: Do you always need a reason to help somebody?
The whole scene where Ash is helping the injured Mewtwo is a genuinely sweet moment, especially when taken in contrast with the First movie.
The scene where Misty and Brock, barely knowing a thing about Mewtwo, immediately jump to defend him from Giovanni and Team Rocket is both awesome and heartwarming at the same time.