List #2 took a little more decision-making on my part. I had to evaluate my current list and make a few choice corrections to reflect my current tastes. But there are still plenty of movies or single-part OVAs to praise, so here's ten more, in short.
ANIME TOP TEN (LIST #2) FOLLOW-UP
11. Farewell Space Battleship Yamato - The most memorable Yamato film, and an early attempt at capping the franchise, this movie has action, drama, romance, and plenty of large scale operatics.
12. Nausicaa of the Valley of the Wind - Miyazaki does what he does best in this adventure film with an environmental message. He transports the viewer to a foreign world, filled with wonder and danger, but without alienating the audience.
13. Lupin III: Episode 0: First Contact - This is probably the quintessential Lupin adventure, the jewel in the crown of Lupin's grand age of TV specials and embodiment of Lupindom. Not only does it provide the story of how the Lupin gang met, but it's also an exciting, funny romp through New York City, Lupin style.
14. Final Yamato - The climactic (then) final chapter of the Yamato franchise, Yamato goes again on a large scale mission, it's last, to save the Earth from a Noahic disaster. Emotions run high, as does melodrama, but all in all a fine conclusion to the Yamato story.
15. Princess Mononoke - Another gorgeous, sprawling, sweeping story about so many things, such as perserverence, mercy, the environment, and coming of age, Miyazaki again hits a home run as he teaches us all the importance of respecting natural forces.
16. Lupin III: The Fuma Conspiracy - A lot like Castle of Cagliostro, but maybe not quite as beautiful. It does have the advantage of being more Lupin-ish than Cagliostro, with the characters acting a bit more like their usual selves. But also like Cagliostro, it has quite a bit going for it as an adventure movie.
17. Patlabor: The Movie - Though not quite as complex as the second movie, the first Patlabor movie plays as a more mature version of a regular episode of the OVA, pitting Noa Izumi, Asuma Shinohara, and others against a bigger threat than they're used to, involving the very Labor robots they're tasked to use in their jobs.
18. Macross Plus: Movie Edition - My preferred version of Macross Plus, with a bit more narrative flow and more phenomenal visuals than you can shake a Valkyrie at.
19. Summer Wars - A joyful romp in a visually appealing version of cyberspace and also a look at families and family bonds.
20. (TIE) Lupin III: Alcatraz Connection and Lupin III: One Dollar Money War - Two excellent Lupin adventures directed by Hideki Tonokatsu, that involve a lot of great maneuvering by protagonists and antagonists alike. Definitely two of the best entries in the franchise.
So, with both lists done, there you have it, a good portion of my tastes.