Almost all of the manga consists of stories about Ayanami Rei.
List
Ayanami 1 Gakusei Hen [eng]
Ayanami 2 Hokenshitsu Hen [eng]
Ayanami 3 Sensei Hen [eng]
Ayanami 4 Boku no Kanojo Hen [eng]
Ayanami 4 Preview Edition [eng]
Ayanami 5 Meirei Hen [eng]
Ayanami [eng]
Ayanami Dai 1 Kai [eng]
Ayanami Dai 2 Kai [eng]
Ayanami Dai 3 Kai [eng]
Ayanami Dai 3 Kai Pure Han [eng]
Ayanami Rei 00 [eng]
Bakunyuu Maid Kari Kouhen [eng]
Bakunyuu Maid Kari Zenpen [eng]
Chou Soreyuke Melfina-san [eng]
Evangelimoon [eng]
Hira Hira Dokin Cho [eng]
Maid-san no Hon Boku no Imouto Hen [eng]
Omake Bon Sono 1 [eng]
Omake Bon Sono 2 [eng]
Omake Bon Soushuuhen Sono 1 [eng]
Omake Hon [ENG]
Omake Hon 2006 Natsu [English]
Rei Ayanami Rei [eng]
Under Ground [eng]
NEW!! :
Ayanami Dai 3 Kai [English] [Uncensored]
Ayanami Dai 3.5 Kai (Neon Genesis Evangelion) [English]
Bonus Book Summer 2010 [English]
Gentei Omakehon 2005.2 [ENG]
Limited Edition 2006 Winter (Evangelion) [English]
Natsu Omakebon (Neon Genesis Evangelion) [English]