I like that the OP’s list includes two cartoons that make extensive use of 3D animation. 
Do you mean Futurama and The Iron Giant? Because I don’t recall much, if any, 3D animation in there. They did use computer animation, but used it to mimic traditional 2D drawings.
The feature length Batman movies were all pretty good:
Batman: Mask of the Phantasm
Batman: Subzero (what “Batman & Robin” could have been)
Batman/Superman: World’s Finest: The scene where Superman finds the Bat-tracker on his cape is hilarious
Batman: Mystery of the Batwoman
Batman Beyond: Return of the Joker (original edit)
Nitpick: Although Tex Avery’s nuttiest and most memorable cartoons were done at MGM, the Tom and Jerry shorts were the work of two guys…you know. They named a studio after themselves later on. Bill Whathisname and Joe Somethingorother.
Johnny Quest. Particularly the episode with the giant spider. simh simh salabimh!
Beany and Cecil. A Bob Clamp-ett car-tooooooooooon!
In no particular order:
Rocky & Bullwinkle
George of the Jungle
Simpsons
Futurama
Beauty and the Beast
Aladdin
Quick vote for Howl’s Moving Castle. I enjoyed it more than Spirited Away, possibly because it’s more of a Western fairy tale than an Eastern one, so more familar. That and I just loved the way it looked. Have to get it on DVD.
I highly recommend Cat Soup to all of you animation fans. I’ve watched it a dozen times and I come away with something new every time. Incredible.
I liked Mission Hill, The Oblongs, and Time Squad.
The only japanimation series I liked and watched with some regularity was Samurai Pizza Cats.