Here are the box office rankings of the anime movies in the first half of the year 2011. According to Anime!Anime!, Doraemon, One Piece and Precure movies were severely affected by the earthquake in March. 107 theaters temporally suspended the running of Doraemon movie due to the damages to the buildings. Toei Animation omitted scenes of Tsunami from the Precure DX3 movie.

rank/ box-office revenue by yen/ number of screens/ title ($1 = 78 - 80 yen)
*1, 3,130,000,000 332scr Detective Conan Movie 15: Quarter of Silence
*2, 2,440,000,000 275scr Doraemon: Nobita and the New Steel Troops - Angel Wings
*3, 1,770,000,000 173scr Inazuma Eleven: Saikyou Gundan Ogre Shuurai
*4, 1,340,000,000 351scr Pokemon Best Wishes! the Movie
*5, 1,200,000,000 325scr Crayon Shin-chan Movie 19: Arashi wo Yobu Ougon no Spy Daisakusen
*6, 1,150,000,000 457scr Kokurikozaka Kara (running)
*7, 1,020,000,000 130scr Eiga Precure All Stars DX3: Mirai ni Todoke! Sekai wo Tsunagu Niji-iro no Hana
*7, *,790,000,000 125scr One Piece 3D: Mugiwara Chase & Toriko 3D: Kaimaku Gourmet Adventure!!
*8, *,700,000,000 101scr Macross Frontier: Sayonara no Tsubasa
*9, *,600,000,000 279scr Tezuka Osamu no Buddha: Akai Sabaku yo! Utsukushiku (running)
10, *,470,000,000 *90scr Fullmetal Alchemist: Milos no Seinaru Hoshi (running)
11, *,387,000,000 422scr Toufu Kozou
12, *,330,000,000 107scr Cheburashka & Kuma no Gakkou: Jackie to Katie
13, *,250,000,000 *60scr Ghost in the Shell: Stand Alone Complex - Solid State Society 3D
14, *,250,000,000 *22scr Sengoku Basara: The Last Party (running)
15, *,151,000,000 132scr Sore Ike! Anpanman: Sukue! Kokorin to Kiseki no Hoshi
16, *,100,000,000 *60scr Hoshi wo Ou Kodomo (running)
17, *,*90,000,000 *85scr Onigamiden
18, *,*85,730,000 137scr Nintama Rantarou Movie: Ninjutsu Gakuen Zenin Shutsudou! no Dan
19, *,*57,200,000 *35scr Sora no Otoshimono: Tokeijikake no Angeloid (running)

Sources: Anime!Anime!, Box Office Mojo, Eiga.com, Bunka Tsushin