I haven't seen anyone mention Wallace and Grommit yet, or for that matter Chicken Run.
I think i wore out my copy of Disney's Robin Hood when i was a child.
I know Pixar just released most of their "shorts" on a compilation DVD.
The visuals and production design for the most recent Peter Pan were pretty stunning. Not as great as a whole as teh classic but visually just stunning.
that's all i can think on right now other than the obvious pixar and classic disney recommendations.
I would definitely recommend Pixar's "shorts" as well, my son has watched pretty much all of them, and liked them all.
If she likes the Spongebob series, she may like the movie as well, I know I enjoy watching as well.
Also, as mentioned above, the Studio Ghibli Anime's are also very entertaining, I grew up in Japan, and those movies were a big part of my learning Japanese, while being fun to watch.
And the Thomas the Tank Engine series, he loves those too. But maybe because he is on a train kick at the moment. Might be a little too slow and quiet for your daughter's tastes.
Is Iron Giant good for a three year old though? Not so sure. Secret of Nimh was a favourite of mine. Looking on Amazon (and thinking of the intended audience), what about The Last Unicorn or Fern Gully? Seems like stuff for a little girl to enjoy.
Robin Hood FTW, deffo the Disney version for kids. When I was tiny I was raised on Robin Hood, King Arthur and PIRATES! later, Sherlock Holmes (c. six-ish).
Like one of the above, I also really enjoyed the latest Peter Pan (although why was Peter Pan the ONLY American character in it?).
I also remember liking The Sword In The Stone when little, even had it on tape so I could listen to it in my room when not downstairs with the telly. Liked it recently too, so good one to watch with kids.
My neighbours let their tiny kid watch Star Wars and LOTR. Not sure I personally recommend it, but whatever, you know? My Classics teacher let his kids watch South Park until they learnt to speak, because they enjoyed the bright colours and fart sounds. And all the poo...