Every time Hammer is around, of course... especially when Mina gets scared upon her first sight of him, calling him "the man with thousands of weapons". Doubles as a reference to Musashibo Benkei. Sadly, Lost in Translation in the dub, though they worked in a pretty good running gag of everyone thinking Hammer's nuts to run a weapons shop in Dracula's Castle.
Some of the enemy descriptions, such as Lubicant: "Always angry demon of Hell. Not enough calcium in its diet."
The depiction of Excalibur as The Sword Still In The Stone. Soma's somehow strong enough to swing it with the stone still stuck on and whack enemies with it anyway.
Spam crouch rapidly. Soma will look like he's rocking an epic Air Guitar solo.
One of the rooms has nothing but a single Killer Fish left upside down out of water, and nothing else. No water, no items, just a single fish out of water. This is usually the one players will use to get the Killer Fish soul.
Anytime it is suggested that Soma and Mina are a romantic couple, Soma gets really defensive. Yoko has a lot of fun with this.
There's also the sheer audacity of Alucard making an alias for himself by using his own name spoken through a Japanese Ranguage filter.
The Killer Doll's soul allows Soma to throw a doll that looks like himself or Mina which distracts enemies. Seeing enemies attack and sometimes completely miss the doll is bound to earn some chuckles.