Sanae's chapters giving her a Metroid-style theme, including Theme Music Power-Up when obtaining new gear. Not to mention the final boss of her final chapter, which mixes Cave Story, a borderline Metroidvania indie game, into the music starting at the cutscene before the fight. The fight basically has Touhou characters, a Mother gameplay system with Metroid elements while Cave Story music plays in the background, being lightly influenced by Kanako's theme, as well. Four series/games in one. YES
The battle against Mima near the end wherein Marisa learns her ultimate ability. The sudden beginning and absolute musical swelling of Reincarnation only adds to it.