I'll range by games I guess.
Touhou 6: Hard to find anyone, but as the previous poster I'd head towards Patchouli or maybe Meiling (that is for named characters). Other from that, the obvious choices are Dai and Koa, though Touhou 6 is a hard thing to digest due to its popularity so even the underrated characters from Th6 still get more recognition from the games below.
Touhou 7: A bit easier task. Letty, Prismrivers and possibly Chen.
Touhou 8: Wriggle, Keine (Unsure because she gets recognition thanks to Mokou), Tewi.
Touhou 9: Medicine (not a hard choice), Eiki (I'm walking on a thin ice here, but that's mainly because this is her only appearance in games apart from end screens and Phantasmagoria games are often forgotten, though Eiki is often brought up because she is a final boss).
Touhou 10: Aki sisters (Shizuha has it harder from Minoriko though), Hina.
Touhou 10.5: Iku (Heavily overshadowed by Tenshi. This is the only instance of a spinoff with two new characters).
Touhou 11: Kisume, Parsee (I kinda disagree, but overall she is just there, isn't she? That could probably apply to Yamame, but from my experience she has at least a bit more recognition).
Touhou 12: It's hard to pick anyone, but I'll go with Unzan, I mean Ichirin, Shou and Nue!
Touhou 13: This is where it gets a bit tricky for me due to these games still being more recent from the past ones so characters from here on now have still a chance to shine in the fandom... Anyway, Kyouko is sometimes forgotten, but she's held greatly by her relation with Mystia, so... Tojiko. Definitely Tojiko. Maybe Yoshika too, but she's also held, by Seiga.
Touhou 14: Tsukumo sisters. That's about it. The first three youkai have a really big recognition and later bosses do too. Maybe Raiko is also a bit forgotten, but not as much as Yatsuhashi and Benben
Touhou 15: Seiran and Ringo? That's it.
Touhou 16: Nemuno.
Touhou 17: Eika was kinda popular at first, but she got forgotten pretty quickly, didn't she? Same with Urumi. Other from that, everyone else seems to have it easy.
Touhou 18: irefuseitsstilltooearlytomakesuchassumptionskthx Takane, Sannyo, Misumaru, Momoyo.
Spinoff characters are generally forgotten too, like Suika at times (I guess I could put Yuugi in Th11 section, but she got back up I think). Print works characters - I don't know how do they do, but I think Akyuu, Kosuzu, Rinnosuke and Kasen are fairly popular.