Ho Yay: Porthos and Aramis, all over the place. They clearly have a closer relationship with each other than they do with Athos (high-fiving with their swords, for one), which really comes out in the "there is a God" scene.
Narm: The way Cardinal Richelieu was defeated was just weird. He says "Wait!" before Aramis could attack him, and what does Richelieu do next? Give off a big smile. Just...what?