Chizuru: We could talk about it later, but right now...
Saito: No, it would not serve its purpose if it is not now.
At the end of the episode, he finally manages to say it, but by that point the moment is long gone and Chizuru, distracted by other subjects, thinks he's talking about what Hijikata would look like with a beard.
After all hell has broken loose at Sumiya, Hijikata grabs Chizuru and makes a run for it - only to be stopped at the gate by a well-meaning bystander who takes Chizuru for the geiko she's dressed as and assumes Hijikata is either kidnapping her or trying to elope with her. Trying to explain goes nowhere fast and Hijikata quickly loses it, announcing his identity as Vice-Commander of the Shinsengumi and declaring that Chizuru is under his protection, resulting in widespread rumors that Hijikata Toshizo, Vice-Commander of the Shinsengumi, has eloped with a cute geiko.
Okita is waiting back at headquarters when Hijikata returns with Chizuru, still dolled up in geiko attire, in tow. Judging by his smug greeting, one almost gets the impression he knew something like it would happen when he originally suggested the whole idea of having Chizuru spy for them.
Okita steals Hijikata's book of haiku and gleefully avoids Hijikata's efforts to grab it from him, playing keep-away with it in front of the rest of the Shinsengumi captains and Chizuru.
From the drama CDs, Okita has yet again stolen Hijikata's poetry collection and gives it to Saito as a bribe. When Hijikata finds out and asks for it back, Saito, in all earnest seriousness (and presumably with Okita, Toudou, Nagakura, and Harada all listening avidly in the background), asks him about the meaning of one of the lines, to Hijikata's intense embarrassment.
Later, after Hijikata has taken the book back and ordered Saito never to ask him about it again, Okita consoles Saito by telling him that he's memorized the whole thing and offering to recite it for him. Which he does next to an open window. Loudly.
From the same drama CD, all interactions between Hijikata and Souji. Bonus points to Kondou seeing their arguing as Souji acting like a cute younger brother, much to Hijikata's disgust.
Also from the drama CDs, "The Two Toshizos": Okita adopts an injured stray cat and, because he's a troll, names it "Toshizo" after Hijikata. When Saito and Nagakura find out, Saito cannot bring himself to use Hijikata's given name even to talk to a cat and resorts to calling the cat "Vice-Commander" instead - and when Kondou happens to overhear Okita, Nagakura, and Saito discussing the feline Toshizo's habits of stealing food, sneaking into people's beds, and siring children around the neighborhood, he assumes they're talking about Hijikata and confronts him about it.
Someone took the audio from the drama CD and made a fanvideo. It's utterly hilarious. Found here.
The Shinsengumi health inspection, specifically Nagakura enthusiastically showing off his muscles to Dr. Matsumoto while the latter patiently tries to move him along.
Sanosuke gets drunk and shows off the scar from his BungledSeppuku. Shinpachi paints a face on it. In the anime adaptation, there's a dance involved that leaves Heisuke and Shinpachi rolling on the floor with laughter.
When the Shinsengumi first adopt their Western-style uniforms, Chizuru realizes that Saito has buttoned his coat wrong. Having her point it out to him causes the normally stoic Saito to become flustered with embarrassment, and he awkwardly says that he'll fix it later.
In Heisuke's route, Chizuru is so startled by how he looks in the new uniform and short hair that she calls him "sexy" out loud, which touches off a brief interval of flirting that lasts until Hijikata, also in the room, exasperatedly tells Heisuke to stop showing off.
Chizuru revealing she's a girl early in the game, causing sudden dead silence.
Nagakura: Girls don't wear pants!
In the Drama CD "Sword Appraisal", Heisuke needs a new sword after Ikedaya, so Souji and Saitou try to help him out. Key word: try. It quickly escalates into an argument over whose sword is better, Kondou's or Hijikata's, and when Heisuke tries to intervene, we get this gem from Saitou:
Saitou: You can't tell the difference anyway. Close your eyes and grab one you like.
Three words: Ishida Powdered Medicine.
Some of the trophies you can get from Playing Stories of the Shisengumi on the PS3 have hilarious titles. Some of these are That Got Dark Fast, Huh for getting the normal ending, On My Toudou List, It's Always the Quiet One and Ronin on the Streets, Samurai under the Sheets from completing Saito and Harada's routes, respectively.
Harada, Shinpachi and Heisuke's attempted sneak out to Shimabara. From Chizuru pointing out it's too early to go to the red-lights district and Harada's response that "it's every man's dream", to Inoue inadvertly twarting their plans with training and Heisuke and Harada using Chizuru as a scapegoat and abandoning Nagakura with Inoue.