Obviously, Pixar and Studio Ghibli own this thread. No one has made animated movies better than those two studios, including Disney. Yes, Disney is currently doing better than Pixar, but Disney's best still pales in comparison with Pixar's best.
In addition to the best of Pixar and Studio Ghibli, these are the animated movies I've enjoyed the most:
Summer Wars
The Girl Who Leapt Through Time
Wonder Woman
Batman Beyond: Return of the Joker