It's all but Touhou Project tradition for at least one Ensemble Darkhorse to arise per game:
Embodiment of Scarlet Devil
- The Embodiment of Scarlet Devil has Hong Meiling, who for a long while was the most popular minor character that was never playable. After several debates about what to call her since it was initially unclear whether her name should use the Japanese or Chinese reading of the kanji (which ended with everyone calling her "China") she garnered enough popularity that, at one point, she took the top spot in the game's equivalent of Saimoe. Her popularity led to her being included as a playable character in the first fighting Gaiden Game of the series, but due to her Butt-Monkey status she became a Joke Character with no role in the storyline, and with Hisoutensoku returned to playable status as well as finally getting her own story route (she still didn't escape being a Butt-Monkey, though).
- Cirno is the Ensemble Darkhorse of Touhou, Memetic Mutation (she's the strongest and a genius!) propelling her into perpetual stardom amongst the fans. This led not only to her being playable in Hisoutensoku but also one of only three with a story route (along with Meiling and Sanae), and with Great Fairy Wars managed to get her very own game.
- Cute, destructive Flandre Scarlet is featured just as much, if not more, in fan works than the other members of the Koumakan Cast Herd, despite appearing in a grand total of one game (and one Gaiden Game that no-one liked).
- And then there's that "little devil" that appeared as a midboss in Patchouli's stage. No dialogue. No name. No profile. Immensely popular. Not quite as popular is the similarly unnamed fairy that appears as the Stage 2 midboss, though that's due almost entirely to her portrayal as being a friend of Cirno (see above). The two have come to be known to fans as Koakuma ("Little Devil") and Daiyousei ("Great Fairy").
- It could be argued that the bosses in this game are this to the entire series considering that they are the most featured in Gaiden Games and supplementary material, and by extension, giving them more characterization. Not to mention that any fanwork that features more then a couple specific characters usually have at least one of them. There's also the fact that out of most bosses, the bosses of this game seems to be the most associated with the main characters, with Sakuya herself being a main character until Mountain of Faith and again in Double Dealing Character.
Perfect Cherry Blossom
- Perfect Cherry Blossom has the Prismriver Sisters. They would later return in Phantasmagoria of a Flower View and frequently appear in various fanworks.
- Lily White, a midboss of PCB, also a special Mook in Phantasmagoria of Flower View, is exceptional enough to have received her own profile in Perfect Memento in a Strict Sense (read: official material)! Ran and Chen are debatable depending whether you view Yukari's shikigami as side characters or not. Alice would be considered an Ascended Extra.
- Imperishable Night has Tewi Inaba, and Fujiwara no Mokou. Also Reisen, which depends on whether you view her as a main character or a side character.
Phantasmagoria of Flower View
- Phantasmagoria of Flower View has Yuuka Kazami, who is a debatable example as while most of her fans are only familiar with her brief appearance in one game she was also the final boss of Lotus Land Story and playable in Mystic Square (though even that is debatable, as ZUN hasn't confirmed if they're the same character or just him being nostalgic).
- Also from PoFV, "sunflower fairy". While being just a Giant Mook, she does have some popularity and fanart.
Mountain of Faith
- Mountain of Faith has Nitori Kawashiro to a limited degree, especially after her appearance as a supporting character in the following game. Momiji Inubashiri as well, another nameless, dialogueless, official-artless midboss who has as much fanart as most of the main playable characters.
- Subterranean Animism has both Parsee Mizuhashi and Yuugi Hoshiguma. May have something to do with the incredible amount of people that pair them together. Satori Komeiji is also extremely popular; she's been in the top 10 in the annual Touhou Popularity Contest ever since she's been eligible.
- Quite possibly one of the best examples of the series is Komeiji Koishi. In the 11th popularity poll by TH Wiki, she ranked 1st, dethroning even Reimu, who had been occupying the position for 6 years straight. Ironic, considering that in-universe she has the ability to not be noticed by anyone.
Undefined Fantastic Object
- Undefined Fantastic Object has Kogasa Tatara. Partly due to the fanbase quickly latching onto her when the demo was first released, partly due to being the only character not connected to the game's plot at all, mostly due to being immensely cute and pitiable.
- There's also Yoshika Miyako, the Chinese zombie with an invisible steering wheel and the latest Touhou ear worm as her theme. Ten Desires also has The Dragon Mononobe no Futo, notably much more popular than her boss Toyosatomimi no Miko.
Double Dealing Character
- Double Dealing Character brought Seija Kijin: an amanojaku with the ability to flip anything over. This means that she is a Commander Contrarian by nature, and her ability manages to be Boring, but Practical by having one of the lowest bullet counts, but using Interface Screw to make them deadly. She also is responsible for manipulating Sukuna to instigate the events of the game. The very next spin-off actually had her as the main character with her pretty much fighting and beating everyone in Gensokyo while they are fighting without being limited to Spell Card Rules. Essentially making her a near canonical Memetic Badass.
Legacy of Lunatic Kingdom
- Clownpiece from Legacy of Lunatic Kingdom is extremely popular in Western fandom due to her American-flag-printed clothes and spellcards. In the game, she's dressed this way by Hecatia to remind the Lunarians of the time humans landed on the Moon (making her a kind of living Brown Note); to the aforementioned fans, it's an opportunity to mesh Touhou and 'Murrican hyper-patriotism together.
- There are some PC-98 darkhorses as well. They were not necessarily such when they were released, but once Touhou gained its memetic popularity people decided to look at the earlier games and decided these characters need to come back. Mima is persistently on the top of the charts of PC-98 characters that need to come back, being formerly playable, connected to secondary protagonist Marisa, and having mysteries about her backstory and nature (and an awesome theme). Next in line is Shinki, mostly because she may be popular character Alice's mother. Finally Elly gets this because of the "Bad Apple" meme - it's based off her stage theme from Lotus Land Story.