Here's the list I submitted.
1. Nausicaa of the Valley of the Wind (1984, Miyazaki)
2. Toy Story (1995 Lasseter)
3. Toy Story 3 (2010, Unkrich)
4. My Neighbor Totoro (1988, Miyazaki)
5. WALL*E (2008, Stanton)
6. Princess Mononoke (1997, Miyazaki)
7. Whisper of the Heart (1995, Kondo)
8. Porco Rosso (1995, Miyazaki)
9. The Iron Giant (1999, Bird)
10. Paprika (2006, Kon)
11. Beauty and the Beast (1991, Trousdale, Wise)
12. Aladdin (1992, Clements, Musker)
13. The Girl Who Leapt Through Time (2006, Hosada)
14. Grave of the Fireflies (1988, Takahata)
15. Arriety (2012, Yonebayashi)
16. Ghost in the Shell (1995, Oshii)
17. South Park: Bigger, Longer, & Uncut (1999, Parker)
18. Interstella 5555: The 5tory of the 5ecret 5tar 5ystem (2003, Takenochi)
19. Finding Nemo (2003, Stanton)
20. Summer Wars (2009, Hosada)
21. Batman: Mask of the Phantasm (1993, Radomski, Timm)
22. The Incredibles (2004, Bird)
23. Millenium Actress (2003, Kon)
24. The Nightmare Before Christmas (1993, Selick)
25. The Jungle Book (1967, Reitherman)
26. Spirited Away (2001, Miyazaki)
27. Only Yesterday (1991, Takahata)
28. The Castle of Cagliostro (1979, Miyazaki)
29. Howl’s Moving Castle (2004, Miyazaki)
30. Rango (2011, Verbinski)
31. Persepolis (2007, Parronaud, Satrapi)
32. The Secret of Kells (2009, Moore, Twomey)
33. I Can Hear the Sea (1993, Mochizuki)
34. How to Train Your Dragon (2010, DeBlois, Sanders)
35. Mary and Max (2009, Elliot)
36. Ponyo (2008, Miyazaki)
37. Perfect Blue (1998, Kon)
38. Waltz With Bashir (2008, Folman)
39. Toy Story 2 (1999, Lasseter)
40. The Lion King (1994, Allers, Minkoff)
41. Sita Sings the Blues (2008, Paley)
42. Wallace and Gromit: Curse of the Ware-Rabbit (Box, Park)
43. Beavis and Butthead Do America (1996, Judge, Kaplan)
44. Monsters, Inc (2001, Docter)
45. Jin-Roh: The Wolf Brigade (1998, Okiura)
46. Tokyo Godfathers (2003, Kon)
47. Goshu the Cellist (1982, Takahata)
48. Akira (1988, Otomo)
49. Castle in the Sky (1986, Miyazaki)
50. In The Attic (2009, Barta)