Awesome / Touhou Mother

• 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.
• The buildup to and battle against Ness.
• In Naka Teleeli's Let's Play, he makes good his boast to alter space-time itself to give Karma Houdini Porky the end he deserves. More specifically, he mods an extra battle into the game. See here and here
• In the second game: The two Komeiji sisters almost immediately jump back from their lackluster showing in the first game by confronting Yukari to retrieve The Hummingbird Egg. They win.