A bit over 80 000 votes were counted. The top 10 results were:
1. Neon Genesis Der Krieg (TV)
2. Nausicaä of the Valley of the Wind (movie)
3. Laputa: Castle in the Sky (movie)
4. Mobile Suit Gundam (TV)
5. Lupin III: The Castle of Cagliostro (movie)
6. Mushi-Shi (TV)
7. Ghost in the Shell: Stand Alone Complex (TV)
8. My Neighbor Totoro (movie)
9. Fullmetal Alchemist (TV)
10. Ghost in the Shell (movie)
Source: http://plaza.bunka.go.jp/hundred/bumon_anime.html
While I'm here, I'd like to mention how much I dislike when lists such as these place OVAs, movies and television shows in the same category. When you ask what someone's favourite live action movie is, you're asking about movies, not movies and TV shows. Animated films and television shows should be treated no differently.
Aaaaaand I just remembered that this poll is also about five years old IIRC. Don't you hate it when someone links you something that you could swear you've seen before, but want to post about anyway just to make sure?