Dengeki conducted an online poll on the popularity of the anime movies shown in the fiscal 2009. Fans voted for the best anime movie they watched.

*1, Evangelion: 2.0 You Can (Not) Advance
*2, Summer Wars
*3, Macross Frontier ~Itsuwari no Utahime~
*4, Mahou Shoujo Lyrical Nanoha The MOVIE 1st
*5, Tales of Vesperia ~The First Strike~
*6, The Disappearance of Haruhi Suzumiya
*7, One Piece: Strong World
*8, (Up by Disney)
*9, Tengen Toppa Gurren Lagann Movie: Lagann-hen
10, Kara no Kyoukai 7: Satsujin Kousatsu (Part 2)

ref. the box office ranking of the anime movies in 2009.
Rank/ box office/ screens/ weeks
*1, $48,192,309 194scr *7w One Piece: Strong World
*2, $40,631,237 366scr *5w Pokemon Diamond & Pearl the Movie: Arceus - Choukoku no Jikuu e
*3, $40,303,632 109scr 14w Evangelion: 2.0 You Can (Not) Advance
*4, $35,292,488 303scr *8w Detective Conan Movie 13: The Raven Chaser
*5, $23,825,776 288scr *8w Doraemon: The New Record of Nobita - Spaceblazer
*6, $17,425,019 114scr 10w Summer Wars
*7, $11,004,517 311scr *6w Major: Yuujou no Ikkyuu
*8, $10,097,019 153scr *6w Crayon Shin-chan Movie 17
*9, $*9,099,022 146scr *5w Eiga Precure All-Stars DX: Minna Tomodachi - Kiseki no Zenin Daishuugou
10, $*8,341,362 148scr *6w Fresh Precure! Omocha no Kuni wa Himitsu ga Ippai!?
11, $*7,769,864 266scr *3w Naruto: Shippuuden Movie 3 - Hi no Ishi wo Tsugu Mono
12, $*7,522,074 308scr *5w Penguin no Mondai Movie
13, $*6,112,698 311scr *5w Layton Kyouju to Eien no Uta Hime
14, $*6,074,952 *24scr *5w The Disappearance of Haruhi Suzumiya
15, $*4,839,216 *31scr *5w Macross Frontier ~Itsuwari no Utahime~
16, $*4,319,940 213scr *5w Uchuu Senkan Yamato: Fukkatsu-hen
17, $*4,010,476 255scr *3w Eiga! Tamagotchi Uchuu Ichi Happy na Monogatari!?
18, $*3,130,376 211scr *3w Hottarake no Shima ~Haruka to Mahou no Kagami~
19, $*2,444,050 *19scr *3w Mahou Shoujo Lyrical Nanoha The MOVIE 1st
20, $*2,017,918 124scr *2w 10th Anniversary Gekijouban Yu-Gi-Oh! ~Chou Yuugou! Toki wo Koeta Kizuna~
21, $*1,853,535 149scr *4w Anpanman Movie 2009
22, $*1,630,434 *11scr *5w Tengen Toppa Gurren Lagann Movie: Lagann-hen
23, $*1,139,719 144scr *4w Keroro Gunsou Movie 4: Gekishin Dragon Warriors de Arimasu!
24, $**,941,610 *34scr *2w Tales of Vesperia ~The First Strike~ 34screens 2weeks
25, $**,702,155 210scr *1w Yatterman 2008 Movie
26, $**,505,349 **7scr *2w Higashi no Eden - Movie I: The King of Eden
27, $**,400,773 *12scr *1w Fate/stay night: Unlimited Blade Works
28, $**,292,467 *29scr *2w Eagle Talon Movie 3
29, $**,215,163 **1scr *5w Kara no Kyoukai 7: Satsujin Kousatsu (Part 2)

Sources: Dengeki, Box Office MOJO, Anime!Anime!