Read other letters about this article
I didn't respond to the first list, but am grateful that so many I'd thought of made your list.
Before I second some of things in the comments, I gotta say that I don't think either Watership Down, which I think is excellent, or Grave of the Fireflies, which is probably the single most depressing animated film of all time, would be suitable for children. Both are simply too violent for younger children. Watership Down is excellent though and might be held in reserve for the double digits.
The Fleischer Superman - gorgeous painterly art deco animation. A friend has a 2-year-old who regularly asks to come over to watch my Superman cartoons. "Superman! Superman helps!" 66 years old and he loves them.
Into the West - Great Irish film.
MP and the Holy Grail - my mom and I used to bond over this and the regular series. But especially the film. And there's Jaberwocky as well, also Terry Gilliam.
The Great Race - back in the long-ago of the Independent TV Station, KTLA 5 in L.A. would run this as a "special event, and it was another bond with my mom, who loved Curtis and Lemon in this. Great silly fun.
And with Halloween not all that far away, I'd like to recommend two "scary" movies at parent's approval - the Japanese anthology Kwaidan and the SF classic Five Million Years to Earth. The last is still effective and creepy without being violent. My friends and I realized we'd all been terrified by this as kids.