My son is 2 and a half, and so I've been watching a lot of Pixar and Dreamworks recently, so this is slanted that way but...
1. The final dragon duel in "How To Tame Your Dragon.": Brilliant reconciliation scene between a father and a son, and a father and his life long enemy.
2. The first scene of "Up.": If you're over 21, a male, and watch this and don't at least choke up you're a monster. Pure and simple.
3. The final scene of "Finding Nemo.": Seeing the new dynamic between the father and son is pretty neat, and a very solid end.
4. The final scene of "Toy Story 3": See 2, in that if you don't choke up you're a monster.
And some other stuff:
1. The weightless fight in "Inception": Especially impressive as they didn't use special effects.
2. The ending of "Dark Knight": Gordon's narrative to his son makes this scene.
