There are certainly a lot of funny references in the game! My favorite reference was Milo Graytail's similarity to Pinky from "Pinky and the Brain", and I also found the Frogfather very hilarious! Has anybody else spotted some funny references? I'd love to hear about them!
Teah there are nice references, my favourites are:
When you recover San Bonobo hand from a cave in Monquista, the scene is took from Indiana Jones and the Last Crusade with the old monkey "templar knigt" and the choice of the right holy grail, pardon hand .
In Moshuu when you face the good Crimson monks there will be a house with fire elephant oni, when you will defeat them their last dialogue is inspired from the last words of the replicant in Blade Runner .