According to the Touhou Moto Neta Wiki,
Almost all of Nitori's Skills and Spell Cards are a reference to old arcade games. Tasofro's blog probably meant this by "ZUN's naming sense"
Mamizou's three Stage 5 spell cards all reference the same game.
In addition, the fake Miko spell also references the phrase Miko says after "Royal Clan's Chaotic Dance", which probably was a reference to said game, anyway.
Totally unrelated, but Cirno says Hata no Kawakatsu's name in the Extra Stage of th128. Don't know if it was supposed to be foreshadowing or not.
Marisa's 6[6]B, Ichirin's spellcards, Koishi failing 66A, Mamizou's Loss by Popularity(The backache one) would be good gifs, I think.
Really amusing to think how the Touhou version of Mononobe Clan's temple burning changed throughout the series.
In th13, it was referenced in a single spellcard, and the historical events are mentioned in her profile.
In Symposium of Post-mysticism, Miko says that Futo said she was afraid of Buddhist statues, and then burn them down.
In th135, in her Story Mode, Futo says that she has a 'profound relationship' with Buddhism. And then considers setting things on fire.
Byakuren regains a bit of spirit if she 'catches' 'used' X bullets. Quite a subtle special ability. I don't think it's mentioned anywhere.