Note: the canonical term for the "Secret Boss" or "Shadowboss" etc. is actually "Extra Boss", Spamton says it in Chapter 2, which is directly from Touhou!
Chapter 1: Jevil, Flandre Scarlet; This connection is extremely obvious, but I don't see people make the comparison that often. Also, yeah, Jevil ain't coming back later in the game. Sorry.
Chapter 2: Spamton G. Spamton, Koishi Komeiji; This one is certainly a bit more out there, but Koishi's Urban Legend power is extremely similar to Spamton's whole backstory. "Hartmann's Youkai Girl" is sampled in "Your Best Nightmare", alongside "Bad Apple". "BIG SHOT" also contains a small Bad Apple reference.
Chapter 3: The Roaring Knight, Alice Margatroid; "It's all an Alice Allusion? Always has been," Me to myself for (Jackenstein pumpkin) taking way too long to figure out how the Knight fits into this.
Chapter 4: Gerson Boom, Genji; Not an extra boss or a boss at all, actually, but can we as a society acknowledge that Gerson is very much just Genji?
Gerson Boom, Suwako Moriya; ...Although, if we're limiting ourselves to just actual Extra Bosses here, Suwako also fits.
Chapter 5: Unknown, Yumemi Okazaki; Apple Girlington Theory will never die, okay? (Toby references "Strawberry Crisis" in the title of "An Apple Disaster".)
Unknown, Fujiwara no Mokou; "Inferno of Jealousy" really could just be an epithet for Mokou, couldn't it?
Chapter 6: No fucking clue. Give me a break, we know absolutely nothing about it.
Chapter 7, part 1: Friend, Ran Yakumo: Could easily be a totally new character, but this guy is suspicious and Yukari does have a cat...
Toby has gone on record to say that Ran Yakumo is his favorite Touhou character.
Touhou 7 had two extra bosses, the second, Yukari, being called a "Phantasm Boss". Really makes you think, doesn't it?
Chapter 7, part 2: W.D. Gaster, Yukari Yakumo: Toby Fox and ZUN collaborated on two Megalovania x Necrofantasia remixes, just for the record.
Shared "Phantasm" theming. When you think about it, "being shattered across time and space" does match Yukari's putative backstory... Yukari is a physicist, which Undertale's Gaster seemingly was also, assuming he was the one Sans learned from.]
