What are the best-selling anime games in Japan? It would be helpful to see which ones released at the peak of the anime/manga popularity, the genre, etc...
Only listing the one best-selling title of each series I could think of. Some huge series like Slam Dunk and Touch aren't there because they don't have anything relevant in gaming. (Some older titles could be missing as sales tracking doesn't go that far back.)
Publisher data
[FCM] Kinnikuman: Muscle Tag Match <SPT> (Bandai) {1985.11.08} (¥4.900) - * / 1.050.000
[FCM] Doraemon <ACT> (Hudson) {1986.12.12} (¥5.500) - * / 1.150.000
[SFC] Dragon Ball Z: Hyper Transmission <FTG> (Bandai) {1993.03.20} (¥9.800) - * / 1.450.000
[GMB] Yu-Gi-Oh! Duel Monsters 4: Jounouchi Deck / Yugi Deck / Kaiba Deck |GameBoy Color| <TBL> (Konami) {2000.12.07} (¥4.800) - 2.180.000
[PS2] Jissen Pachi-Slot Secrets! Fist of the North Star # <TBL> (Sammy) {2004.05.27} (¥3.990) - * / 1.000.000
Famitsu data
[PS1] Kindaichi Shounen no Jikenbo: Hihoushima Aratanaru Sangeki <ADV> (Kodansha) {1996.11.29} (¥5.800) - 52.925 / 96.021
[PS1] Rurouni Kenshin: Meiji Kenyaku Romantan - Juuyuushi Inbou-hen <RPG> (Sony Computer Entertainment) {1997.12.18} (¥5.800) - 80.784 / 234.675
[GBA] The Prince of Tennis: Genius Boys Academy <SPT> (Konami) {2002.04.25} (¥4.800) - 101.925 / 231.947
[PS2] Fullmetal Alchemist: The Broken Angel <RPG> (Square Enix) {2003.12.25} (¥6.800) - 121.362 / 252.651
[GBA] Crayon Shin-Chan: Arashi o Yobu Cinema Land no Daibouken! <ACT> (Banpresto) {2004.04.16} (¥5.040) - 20.747 / 152.680
[PS2] Berserk: Millennium Falcon-hen Seima Senki no Shou # <ACT> (Sammy) {2004.10.07} (¥7.329) - 44.586 / 83.215
[PS2] Saint Seiya: Chapter Sanctuary <FTG> (Bandai) {2005.04.07} (¥7.140) - 80.748 / 127.509
[PS2] Yuu Yuu Hakusho: Forever <FTG> (Banpresto) {2005.05.19} (¥7.140) - 76.756 / 120.939
Media Create data
[GMB] Hunter x Hunter: Hunter no Keifu |GameBoy Color| <RPG> (Konami) {2000.06.15} (¥4.500) - 69.012 / 103.344
[PS2] Initial D: Special Stage # <RCE> (Sega) {2003.06.26} (¥6.800) - 162.460 / 277.755
[PS2] Hajime no Ippo: The Fighting! 2: Victorious Road <SPT> (Entertainment Software Publishing) {2004.01.29} (¥6.800) - 116.200 / 189.233
[GCN] Naruto: Clash of Ninja 3 <FTG> (Tomy) {2004.11.20} (¥7.140) - 116.964 / 416.750
[PS2] Captain Tsubasa <SPT> (Bandai Namco Games) {2006.10.19} (¥7.140) - 41.708 / 70.426 <79,90%>
[NDS] Death Note: Kira Game <ADV> (Konami) {2007.02.15} (¥5.229) - 44.600 / 103.241
[PSP] Bleach: Heat the Soul 5 <FTG> (Sony Computer Entertainment) {2008.05.15} (¥4.980) - 39.403 / 102.000 <55,73%>
[NDS] Detective Conan: Aoki Houseki no Rinbukyoku <ADV> (Bandai Namco Games) {2011.04.21} (¥5.040) - 19.786 / 62.212 <50,79%>
[PS3] One Piece: Pirate Warriors # <ACT> (Bandai Namco Games) {2012.03.01} (¥8.190) - 655.774 / 830.354 <92,07%>
[3DS] Attack on Titan: Humanity in Chains <ACT> (Spike Chunsoft) {2013.12.05} (¥5.800) - 93.471 / 319.498 <72,03%>
[PS3] JoJo's Bizarre Adventure: All-Star Battle # <FTG> (Bandai Namco Games) {2013.08.29} (¥7.980) - 425.718 / 505.745 <80,95%>
[PS4] My Hero: One's Justice <FTG> (Bandai Namco Games) {2018.08.23} (¥7.600) - 16.026 / 31.080 <81,93%>
[NSW] My Hero: One's Justice <FTG> (Bandai Namco Games) {2018.08.23} (¥7.600) - 24.626 / 62.802 <78,00%>