In Toy Story, of course Flying with Style is just incredible. I would also say the Christmas scene at the end. 
It’s good to see Buzz and Woody be friends, and a lot of humor in this scene.
In A Bug’s Life, the scene I always remember best is not a happy or funny one. My personal favorite scene is Hopper giving his speech ton the ants after Flik destroys the food supply. We see what a threat hopper really is, and we see(hear?) a brilliant display of Kevin Spacey’s acting capabilities.
In Toy Story 2, “When Somebody Loved Me” is really the heart of the film. I always remember this scene as when I fell in love with Jessie’s character. At first I hated her for how she talked to woody, and this scene made me think otherwise. This was also the first time I remember thinking a character was “interesting”, as opposed to simply liking them.
In Monsters, Inc., I would say the scene where Sulley accidentally scares Boo. It changes his perspective on scaring, and Boo, for one time, runs from Sulley instead of to him.
In Finding Nemo, I would say when all the fish and birds are talking about Marlin looking for Nemo, until Nemo himself hears it. the swell of music is so beautiful, and Nemo finally realizes how much his father loves him: he would choose him even over his own fears.
The Incredibles is a very difficult one for me to decide on. I’ve seen this movie so many times over the years I can’t even look at it as a movie anymore; it just seems like part of life, if that makes sense. The scene that affects me the most is when they land in the city, and Helen and Bob fight for the last time. We see how vulnerable Bob truly is. We can assume how much he loves his family, but this scene is a perfect example of showing, not telling. His priorities have finally become clear: his future with his family means more to him than his past with his super suit. How can one not be moved by that?
In Cars, it’s when Lightning pushes the King to the finish line. We see all that Lightning has learned in this simple act of putting someone else before himself.
In Ratatouille, it has to be Ego’s speech on criticism and art. Several moments in the film come close, but this message has to be highlighted. It is also of note that in these lines, Ego reveals how kind he really is.
I haven’t watched Wall-E in a while. But I would point out the scene where Captain McCree is asking the computer for definitions of words that seem quite common place. The humans aboard the Axiom have truly lost their humanity. They don’t know what real food is. They don’t know what it’s like to walk around as opposed to floating. This reminds me of us today… Our food is mostly processed and fake, with added ingredients and preservatives. How often do we walk from one place to another? Are we losing out humanity?
In Up, it has to be when Carl reads Ellie’s adventure book and decided to go back for Russell.
In Toy Story 3, I would pick the scene where the toys realize what a bad place Sunnyside Daycare is. AGAIN, they have made the wrong decision in scorning and ignoring Woody. Woody may not have been right about Andy, but he was right about that day care.
In Cars 2, I guess it’s when Lightning apologizes to Mater and calls him the bomb. Though this movie is so much a comedy, it’s hard for me to see it having a point, less so a scene where we realize the point.
In Brave, it’s when Elinor and Merida return to the witch’s cottage and she isn’t home. For the first time, Merida has to take responsibility for her own actions and try to set things right.
In MU, (If I remember the movie correctly; I never watched it a second time), it’s when Mike realizes he isn’t meant to be a scarer, in the camp(?).
In fact it’s the only Pixar film I haven’t yet watched. Don’t know why, I’ll have to give it a try soon.