The fight against the Core, not to mention the music.
Raiding the Sacred Grounds with Curly strapped on your back who giving you some GREAT cover while a great music plays and the story of Ballos unfolds. The two bosses at the end, the Heavy Press and Ballos, are both amazing fights, as well.
The fact that this game was created entirely by one person. From scratch. Including the game engine and music software.
