I’ve relied on ~8 Wikipedia category articles and Goodreads lists to supply over 440 manga titles assigned uniquely into the categories shōnen, shōjo, seinen, and josei, and I’ve sorted them based on their first volume’s Goodreads stats (the log of the number of raters multiplied by the cube of their score expressed as a percentage). Obviously, dubious categorizations as well as biases inherent in the ratings are problems in the results. Still, the top 50 titles in each category and in all categories combined are given below, as usual minus any actual data from Goodreads.

50 popular manga

Fullmetal Alchemist
Death Note
Attack on Titan
Ouran High School Host Club
One Piece
Fairy Tail
Naruto
Black Butler
Tokyo Ghoul
Maid-sama!
Dragon Ball
Blue Exorcist
Fruits Basket
Rurouni Kenshin
Bleach
Hunter x Hunter
OnePunch-Man
Kamisama Kiss
Soul Eater
Skip Beat!
InuYasha
Sailor Moon
Akira
Case Closed
Electric Daisy
Hellsing
Yotsuba&!
Kimi ni Todoke: From Me to You
Cardcaptor Sakura
Oyasumi Punpun
Love So Life
Berserk
Horimiya
Vampire Knight
Naoki Urasawa’s Monster
Yu Yu Hakusho
Nana
D.Gray-man
Beast Master
Hana to Akuma
Hana-Kimi
Pandora Hearts
Blue Spring Ride
Gakuen Alice
Trigun Maximum
Alice in the Country of Hearts
xxxHolic
Reborn!
Love★Com
Ranma ½

50 popular shōjo manga

Ouran High School Host Club
Maid-sama!
Fruits Basket
Kamisama Kiss
Skip Beat!
Sailor Moon
Electric Daisy
Kimi ni Todoke: From Me to You
Cardcaptor Sakura
Love So Life
Horimiya
Vampire Knight
Beast Master
Hana to Akuma
Hana-Kimi
Blue Spring Ride
Gakuen Alice
Alice in the Country of Hearts
Love★Com
Faster than a Kiss
From Far Away
Special A
Kitchen Princess
Beauty Pop
Orange
Suki-tte Ii na yo
Last Game
The Wallflower
High School Debut
Tokyo Crazy Paradise
Black Bird
MeruPuri
Shugo Chara!
Tonari no Kaibutsu-kun
Akatsuki no Yona
Daytime Shooting Star
Snow White with the Red Hair
Fushigi Yûgi: The Mysterious Play
Boys Over Flowers: Hana Yori Dango
Happy Cafe
1/2 Prince
Dawn of the Arcana
Full Moon O Sagashite
Kodocha: Sana’s Stage
Absolute Boyfriend
Natsume’s Book of Friends
D.N.Angel
Tail of the Moon
Kamikaze Kaito Jeanne
Barajou no Kiss

50 popular shōnen manga

Fullmetal Alchemist
Death Note
Attack on Titan
One Piece
Fairy Tail
Naruto
Black Butler
Dragon Ball
Blue Exorcist
Rurouni Kenshin
Bleach
Hunter x Hunter
OnePunch-Man
Soul Eater
InuYasha
Case Closed
Yotsuba&!
Yu Yu Hakusho
D.Gray-man
Pandora Hearts
Reborn!
Ranma ½
Bakuman
Trigun
Sword Art Online
Assassination Classroom
Pokémon Adventures
Magi: The Labyrinth of Magic
Shaman King
DRRR!! Durarara!!
Code Geass: Lelouch of the Rebellion
Azumanga Daioh
The Legend of Zelda: Majora’s Mask
Hikaru no Go
Rave Master
Chibi Vampire
Koe no Katachi
Tegami Bachi
Yu-Gi-Oh!
Rosario+Vampire
The Ancient Magus’ Bride
Akame ga KILL!
The Devil is a Part-Timer!
High School DxD
Cross Game
The Melancholy of Haruhi Suzumiya
Negima! Magister Negi Magi
Yakitate!! Japan
Love Hina
Cage of Eden

50 popular josei manga

Nana
Red River
The Crimson Spell
Mars
Paradise Kiss
Pet Shop of Horrors
Midnight Secretary
Nodame Cantabile
Solanin
Princess Jellyfish
The Story of Saiunkoku
Tramps Like Us
Bunny Drop
Karneval
Sand Chronicles
Private Prince
Cat Street
7 Seeds
Wandering Son
Sensual Phrase
Gokusen
Sakamichi No Apollon
Ōoku: The Inner Chambers
Honey and Clover
A Drunken Dream and Other Stories
The Cain Saga
Chihayafuru
Desire Climax
Little New York
My Lovely Honey
Maison Ikkoku
My Girl
Aria
Butterflies, Flowers
Utsubora – The Story of a Novelist
Oishii Kankei
Kaze Hikaru
Bitter Virgin
Tada, Kimi Wo Aishiteru
Doll
For The Rose
Princess Ai
anata ni hana o sasagemashou
Beautiful People
Model
Deep Love: Ayu’s Story
X-Day
Hanshin
Suppli
Flat

50 popular seinen manga

Tokyo Ghoul
Akira
Hellsing
Oyasumi Punpun
Berserk
Naoki Urasawa’s Monster
Trigun Maximum
xxxHolic
20th Century Boys
PLUTO
Uzumaki
Mushishi
Ghost in the Shell
Chobits
Vagabond
Tekkon Kinkreet
Lone Wolf and Cub
Gangsta.
A Bride’s Story
Parasyte
Chi’s Sweet Home
Buddha
Puella Magi Madoka Magica
Battle Angel Alita
Neon Genesis Evangelion
Liar Game
Vinland Saga
Blade of the Immortal
Higurashi When They Cry
All You Need Is Kill
Angel Beats!
Planetes
Clannad Manga
Blame!
Wolf’s Rain
Battle Royale
Black Jack
Gantz
Showa: A History of Japan, 1926-1939
Elfen Lied
Domu: A Child’s Dream
Black Lagoon
Ode to Kirihito
Chang Ge Xing
Spice & Wolf
The Voices of a Distant Star
Museum of Terror: Tomie
Ajin: Demi-Human
K-ON!
Corpse Party