I'm surprised this hasn't been mentioned...
The Road to El Dorado
I've heard a fair bit of griping from other parents about it. I don't altogether consider it a kid's movie, though. The themes alone definitely suggest an older audience. And it's one of my favorites.
I like most anything from Studio Ghibli and Aardman, respectively, and I like Coraline and Corpse Bride (though I could do without so much singing in the latter). Monster House was pretty good.
But Watership Down, now... I was allowed to watch it when I was six or seven, and images that I saw there have haunted me for years. For a long time, I just remembered it as the movie with all the sad rabbits watching another strangling in a snare while his neck bled from the tightness of it. It's hard to let that go in favor of whatever good might be in it. The thought of it still make s me feel ill. I came across the song from it (Bright Eyes - Art Garfunkel) a few years ago by another route and was horrified by it, not only the very dark lyrics but something about it that frightened me and made me feel as if a dementor had hold of me (sorry, Harry Potter reference for those unfamiliar, and it fits) and only later did I find out it was from Watership Down and it made sense after that. Somewhere deep down, I think I remembered that song. I'm too afraid to listen to it again. Really.
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"Pack up my head, I'm goin' to Paris!" - P.W.
The world loves diversity... as long as it's pretty, makes them look smart and doesn't put them out in any way.
There's the road, and the road less traveled, and then there's MY road.