Runner-ups are:

Toy Story 1 to 3 are the most beloved ones for me. Apart from the nostalgia, they are so perfectly made. Funny, emotional, entertaining... all in one package.

Up is another one I love, and it always hits me in the feels,

Over the Hedge has to be another I never get tired of watching.

The Hunchback of Notre Dame is epic. A kid's movie with a dark, obscure overtone.

Titan A.E. can be another of those movies I loved and grew up with.

And if Who Framed Roger Rabbit applies, count it in too.

How could've I forgotten about A Monster in Paris if I have it as an avatar and signature?

Good, good!

I can't pick one, so I'll just list a few of my favourites:

Batman: Mask of the Phantasm
Batman: Assault on Arkham
Lion King I and II
Wreck-It Ralph
Meet the Robinsons
The Simpsons Movie

IMO, the recent Big Hero 6 is just Meet the Robinsons 2.0... 

Up
Princess Mononoke
Iron Giant
Laputa Castle in the Sky
Ninja Scroll

I like animated shows/movies usually more than live-action

This masterpiece

Big Hero 6 was alright. I just fell in love with Meet the Robinsons. It might be partly due to nostalgia, but the movie still stands out for me.

I think both have cool music and are quite good overall, but I thought it was strange how close BH6 resembled MtR.

>quirky, genius inventor kid whose parents are absent/dead

>call to adventure leads him to build something new and enter it into a science fair

>science show is where things go wrong

>Plot twist: the villain turns out to be a betrayer, someone who before seemed harmless and has associated with the protagonist in the past.

1) Wolf Children: Ame & Yuki.

2) Summer Wars

3) Spirited Away

4) 5 Centimeters per Second

5) Nausicaa of the Valley of the Wind