Kenshin X Kaoru from Rurouni Kenshin
Yahiko X Tsubame from Rurouni Kenshin
Sanosuke X Megumi from Rurouni Kenshin (my favorite manga, so yeah XD)
Raimei X Kouichi from Nabari no Ou
Ukyo X Heroine from Amnesia
Kaori X Kousei from Shigatsu wa Kimi no Uso
Tohru X Kyo from Fruits Basket (so many ships from that manga XD)
Sakura X Sayoran from Cardcapter Sakura (their love story is really made amazing in TRC too)
Train X Saya from Black Cat
(I've got a lot of ships.... O.o)
Yahiko X Tsubame from Rurouni Kenshin
Sanosuke X Megumi from Rurouni Kenshin (my favorite manga, so yeah XD)
Raimei X Kouichi from Nabari no Ou
Ukyo X Heroine from Amnesia
Kaori X Kousei from Shigatsu wa Kimi no Uso
Tohru X Kyo from Fruits Basket (so many ships from that manga XD)
Sakura X Sayoran from Cardcapter Sakura (their love story is really made amazing in TRC too)
Train X Saya from Black Cat
(I've got a lot of ships.... O.o)