To offer a slightly different list, I generally have a preference for ‘unique’ heroines. These aren’t necessarily the ‘best’ characters in the game, or the ones with the best routes, but they are one of the major reasons that I enjoyed the game(s) they’ve appeared in. (we also need a separate thread for male characters )
A few that immediately come to mind (in no particular order):
Furukawa Nagisa - CLANNAD
Kurihara Touko - Tenshi no Inai
Sumadera Yukio - Tenshi no Inai
Kujou Tamaki - Mugen Kairou 1 (and 2)
Kujou Kaoruko - Mugen Kairou 2 (and 1)
Usami Haru - G-Senjou no Maou
Hirasaka Hatsune - Atlach=Nacha
Sumiyoshi Sakuya - Yumemishi
Sumi Noriko (Don-chan) - Sakashiki Hito no Miru Kokoro + Don-chan ga Kyuu
Aoi Sakuya - Rough Sketch - She sings at the end of the world.
Sakura Nanako - Sakura Sakura