Generally speaking, any time Kasuga go all deredere when she's with Kenshin. Hilarious and CUTE at the same time.
Toshiie's and Matsu's route in SB1 & 2 are both presented in a silent movie-esque style cutscene. Matsu's scenario always has her doing a Magical Girl transformation before going into battle. Complete with hearts and poses!
Matsu's route in 2 starts with both Toshiie and Keiji eating everything in their home, so she and Toshiie has to go to the battlefield to collect ingredients for their dinner. The last stage involves taking vegetables that have the face of Pontiff Xavi, and the whole mission is about Matsu running away from Xavi's fanatics, which includes Motonari and Yoshihiro. That's already funny enough as it is, but it's even funnier when Toshiie and Keiji finally eat dinner from all the ingredients collected, including the Xavi veggies. They got stoned and passed out afterwards.
Toshiie's route on the other hand starts with him taking a hot bath. Only to find out that the bath is actually cold as ice, completely freezing him solid. When he found out that Keiji's behind the prank, he and Matsu spent the whole campaign looking for him. Then turns out both Toshiie and Keiji planned the whole thing, which causes Matsu to drag both their asses back to their home and scolds them both. This entire campaign is filled with hilarity.
In SB2 Tadakatsu's story, usually when he approaches Ieyasu's kidnapper, Ieyasu is just a background (struggling while yelling Tadakatsu's name) while the enemy is doing their normal pose. In the final stage, Tadakatsu's facing Hideyoshi, who's surprisingly silent and not doing his pose. Then he raises his hand slowly... and delivers a Dope Slap on Ieyasu's helmet, he finds Ieyasu's yapping incessant.
In Heroes, Keiji's first story level has him and Hideyoshi attacking Kenshin at Tetorigawa... in order to hang a huge, hand-made caricature of Kenshin as a fox, complete with Keiji and Hideyoshi running away like two bratty schoolboys after a prank upon doing the act. To cap it all, Kenshin finds the whole thing Actually Pretty Funny.
In Yukimura's SB3 blue path, before facing his rival, he hears Shingen's voice and pauses to think. When he discovers Shingen has recovered and is actually right behind him, he completely breaks down into utterly adorable gibberish. Then gets a much-needed Megaton Punch to the face.
The blue path even starts with a laugh. Yukimura intends to hire the Saika Faction to bolster his forces, and orders Sasuke to empty the entire Takeda treasury to do so. Well...
Yukimura: Why didn't you tell me we were broke?!
Poor Muneshige can never catch a break with his lord Sorin.
He's slapped with an embarrassing conversion name, "Gallop", despite not being a Xavist.
The one time he gives Sorin a piece of his mind, he gets fired/exiled.
Sasuke's snarking comes off a bit petty but amusing as well.
"Godammit. Gates cost money, you know."
"Dammit! I'm all soaked! This is going to chap my delicate skin."
Tsuruhime trying to embrace/kiss Kotaro in variations of the same scene, complete with a sparkling pink background and hearts...only for him to teleport away at the last second, leaving her to fall on her face.
Made even funnier when Ieyasu's just standing there in the background looking confused.
In one of Tadakatsu's routes, the Tokugawa Army bust into Ujimasa's castle to rescue a kidnapped Ieyasu...except Ieyasu wasn't even kidnapped in the first place.
Bonus points for Ujimasa sending Kotaro to explain things to Tadakatsu. The only two characters who NEVER speak.
The conversation between Naotora, Yukimura and Masamune in SB4 if you choose to fight against them on Naotora's path, with Masamune trying to play matchmaker and neither Yukimura nor Naotora reacting too well to it.
Mitsuhide/Tenkai's death animation is him laying face down on the ground with his ass sticking out.
From the anime:
Season 1, Episode 5: Naoe Kanetsugu getting WTFPWN'D by Tadakatsu, and again in Season 2, Episode 3 by Toshiie.
Season 2, Episode 9: Motochika and Masamune coming up with the exact same plan to attack Osaka, only with the roles of who does what being reversed. Then starting a fight over it while protesting how they are nothing alike.
The Season 2 OVA. Are you ready for the MANSTRAVAGANZA?!
Yukimura's absolute obliviousness during that episode. Sasuke appears in his usual outfit plus a mask? Yukimura has no idea who he is. Kojuro appears, wearing his usual outfit and nothing else but a mask? Yukimura has no idea who it is, even though he noticed that they were left-handed, and Kojuro is the only leftie in the Basaraverse. He comes face to face with Shingen, and after Shingen's mask breaks, revealing his face completely, Yukimura assumes that he's Shingen's identical twin brother.
Masamune's exasperated expressions and Only Sane Man tendencies during the whole event was hilarious to see.
Poor Sarutobi unintentionally invokes Masamune's Blood Knight tendencies when he transforms into Yukimura.
The yonkoma from Ran Sei Ran Bu tend to be hilarious and actually hang a lampshade on the Joke Weapons of the characters and more, such as:
Masamune trying to find a more stylish and unique eyepatch ends up wearing Kojuro's cat Tama as one.
Toshiie uses a giant Swordfish to fight soldiers, only to be hit by Matsu because he smells of fish. He then loses his weapon when Matsu cooks the fish for lunch.
Mitsuhide and his giant cutlery: after trying to eat with a straight face, he declares them useless and throws them away.
Kasuga showing off her tambourines and prancing around... before dropping on the floor and claiming that these aren't ninja weapons
Masamune has trouble sleeping... because he can't get the "OYAKATA-SAMA!" vs "YUKIMURA!" screams out of his head!
Nohime notices that Nobunaga's Badass Cape is a little too tattered for a conqueror, so she sews him a new one... cue to Nobunaga marching to battle wearing a new cape with the words "From your wife with love" and a little heart on the back, with Ranmaru doing a Spit Take.
From the manga proper, there's a scene where we see the various lords preparing for the incoming war... except the Maeda (Matsu has to take away Toshiie's food because he's gorging himself), the Shimazu (Yoshihiro wants to sleep a little longer) and the Foreigners (cue to Xavii, on a cliff, asking to the sky why they cant' just be buddies).
Yukimura faces the strongest couple of Maeda Toshiie and Matsu... and the first thing he does is to blush like a schoolgirl and call them "shameless", confusing Matsu. When they're defeated and start cuddling each other, he does it again, this time towards the fourth wall.
In Sengoku Basara 3, Masamune inadvertently helps Itsuki steal weapons from his own men and casually threatens the two soldiers who were chasing them (much to the soldier's horror). The icing on the cake is that Kojuro, after hearing the news, still treats them to a Death Glare for daring to point their weapons at their Lord.
From Gakuen Basara
Yukimura and Masamune somehow swapping bodies episode 8. Leading to the hilarious switch of Kazuya Nakai talking in Yukimura's old fashioned vocabulary, while Soichiro Hoshi adapts Masamune's gruff delinquent infliction.
When a baby is left in front of the school, who finds it? The hilariously mute and stoic combo of Fuma Kotaro and Tadakatsu. Who proceed to amusingly care for it together.