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And I second your plug for Fly Away Home.
More hesitantly, I want to mention an animated film called Titan A.E. The story is pretty intense (early parent/child separation, destruction of home world), but the animation is terrific, and the cast wonderful: Janeane Garofalo, Drew Barrymore, Matt Damon, and John Leguizamo, among others. Now 14 and 11, our kids (especially the boy, who's younger) loved this five or more years ago.
A Little Princess is a little miracle.
Did anyone mention Babe? How 'bout the original Charlotte's Web, with Paul Lynde as Templeton?
Great list, Andrew. I'd also like to see what you left off.