Onimusha/Funny

Guildenstern's first scene. That fact that he's dissecting some poor, hapless human shouldn't necessarily be funny, but Guildenstern's gleeful excitement sends it straight into Dead Baby Comedy.

Guildenstern: "And what's this? Ooh, a liver!"

Unlock Samanosuke's "joke" outfit, the panda suit. Wear it. Watch the cutscenes in an entirely different light.

Gogandantess: (for the umpteenth time) "My name is Gogandantess, the greatest swordsman of all... demons!"

Jubei: "...Could we just get on with this?"

Most of Magoichi and Ekei's confrontations count.
Perhaps unintentional, but Jubei's reaction upon meeting a dying villager at the beginning of the game counts. "Are you alright?!" No, Jubei, the guy's just been peppered with arrows, I'm sure he's feeling just peachy...
- Then, Jubei goes on to say the same line, in the same tone of voice, several times throughout the game. His catchphrase, perhaps?
Giving the Love Potion as a gift to any of Jubei's comrades. Hilarity Ensues.
- It gets better when you give the Tengu Mask or the Naughty Novel to Oyu and combine either of them with the Love Potion.
More fun with alternate "joke" costumes: Jubei and Oyu's 70s-style outfits. Wear them and watch the cutscenes.
Ekei's disappointed reaction when he discovers that the villager's daughter he offered to rescue is not a sexy, nubile young woman, but a baby instead. However, the scene promptly turns into Mood Whiplash when the crying baby triggers bad memories for Ekei.

When Vega Donna orders Heihachi to finish off Jacques... and he refuses. Her outraged reaction sells it.
Samanosuke's panda suit makes a return... and this time it's even better, as, not only does it now have two little panda plushies in the pouch at the front, it also has five different facial expressions, ranging from a sinister grin to giant glistening eyes. Have fun!

When Jubei states that only the Yagyu sword can slay a Genma and tells Soki to stand back. His answer? Slashing down one of them with his sword saying: "Is that all ?". Cue to Jubei's face....