The 11 Highest Rated Anime According to Japanese Fans

HaXXspetten said:
If you want a more extended list, I transcribed the top 100 from Anikore a month or two ago and it looked like this (slightly outdated mind you):

1 Steins;Gate 92.7
2 Code Geass: Hangyaku no Lelouch R2 92.6
3 Bakemonogatari 92.4
3 Code Geass: Hangyaku no Lelouch 92.4
3 Ghost in the Shell: Stand Alone Complex 92.4
6 Clannad: After Story 92.3
7 Suzumiya Haruhi no Shoushitsu 92.1
8 Ano Hi Mita Hana no Namae wo Bokutachi wa Mada Shiranai 91.8
9 Fate/Zero 91.3
10 K-On!! 91.2
11 Chihayafuru 91.1
12 Eureka Seven 91.0
13 Toradora 90.9
14 Shingeki no Kyojin 90.8
15 Sword Art Online 90.7
15 Cowboy Bebop 90.7
17 Angel Beats! 90.6
18 Toaru Kagaku no Railgun 90.4
18 Mahou Shoujo Madoka★Magica 90.4
18 Hyouka 90.4
21 Neon Genesis Evangelion 90.3
21 Tengen Toppa Gurren Lagann 90.3
23 Hanasaku Iroha 90.2
23 Natsume Yuujinchou 90.2
23 Black Lagoon 90.2
26 Clannad 90.1
26 Nisemonogatari 90.1
28 Ghost in the Shell: Stand Alone Complex 2nd GIG 89.9
29 Usagi Drop 89.8
29 Fullmetal Alchemist: Brotherhood 89.8
29 Gintama 89.8
29 Tenkuu no Shiro Laputa 89.8
33 K-On! 89.7
33 Nagi no Asukara 89.7
33 Kaze no Tani no Nausicaä 89.7
36 Ookami to Koushinryou 89.6
37 Durarara!! 89.5
38 Yahari Ore no Seishun Love Comedy wa Machigatteiru 89.3
38 Planetes 89.3
40 Suzumiya Haruhi no Yuuutsu 89.2
41 Mononoke Hime 89.1
42 Psycho-Pass 89.0
42 Macross Frontier 89.0
44 Ga-Rei: Zero 88.9
45 Working'!! 88.8
46 Working!! 88.7
46 Hataraku Maou-sama! 88.7
48 Sakurasou no Pet na Kanojo 88.6
48 Toki wo Kakeru Shoujo 88.6
50 Chuunibyou demo Koi ga Shitai! 88.5
51 Higurashi no Naku Koro ni 88.4
52 Darker than Black: Kuro no Keiyakusha 88.3
53 Tiger & Bunny 88.2
54 Ore no Imouto ga Konnani Kawaii Wake ga Nai 88.1
54 True Tears 88.1
56 Kokoro Connect 88.0
56 Kimi no Todoke 88.0
58 Toaru Majutsu no Index 87.9
58 Toaru Majutsu no Index II 87.9
58 Guilty Crown 87.9
61 Higashi no Eden 87.8
61 K-On! Movie 87.8
63 Nichijou 87.7
64 Kami nomi zo Shiru Sekai II 87.6
64 Byousuke 5 Centimeter 87.6
66 Ookami to Koushinryou II 87.5
67 Minami-ke 87.4
67 No Game No Life 87.4
69 Tari Tari 87.3
70 Another 87.2
70 Mirai Nikki 87.2
70 Baccano 87.2
73 Kaleido Star 87.1
74 Baka to Test to Shoukanjuu 87.0
74 Danshi Koukousei no Nichijou 87.0
74 Katanagatari 87.0
74 Zoku Natsume Yuujinchou 87.0
74 Elfen Lied 87.0
79 Kami nomi zo Shiru Sekai 86.9
80 Saki 86.8
81 Boku wa Tomodachi ga Sukunai 86.7
81 Boku wa Tomodachi ga Sukunai Next 86.7
81 Summer Wars 86.7
81 Natsume Yuujinchou San 86.7
85 Baka to Test to Shoukanjuu Ni! 86.6
86 Lucky☆Star 86.5
86 Death Note 86.5
88 Juuni Kokuki 86.4
89 Densetsu no Yuusha no Densetsu 86.2
90 Monogatari Series: Second Season 86.0
90 Tonari no Totoro 86.0
92 ef: A Tale of Memories 85.7
93 Fate/Zero 2nd Season 85.6
93 Yojouhan Shinwa Taikei 85.6
95 Seitokai Yakuindomo 85.5
95 Air 85.5
95 Mobile Suit Gundam Seed 85.5
98 Ore no Imouto ga Konnani Kawaii Wake ga Nai. 85.4
98 Mushishi 85.4
100 Majo no Takkyuubin 85.3