Shortly before the route split, Chizuru has the option to deliver a message to Saito. When she does, Saito ends up telling her that there are probably two reasons she was chosen: One of the other captains would have stood out, and one of the newer recruits to the Shinsengumi might not be loyal. Chizuru, on the other hand, is both inconspicuous and her loyalty is without question. Aww!
Most of the good endings count, even if they're on the bittersweet side.
The Reimeiroku special where Hijikata becomes sick and everyone does something to try to help him out. Saito picks up medicine despite being sick himself. Okita makes rice porridge. Gen makes sweet bean soup with rice cake (Hijikata's favourite). Heisuke sorts out the paperwork. Ryu brings a citron fruit to cure colds. Kondou wants to do something but everyone else already did it. The best part? Hijikata is smiling throughout the whole interaction with Kondou.
In Shinkai, there's a scene near the end of Chapter 2 (unless you're on the Normal Route) where Chizuru asks Kondou to teach her some swordplay. He agrees and spends the whole day training her, then apologizes when he sees how exhausted Chizuru is. She responds that she's actually very happy, which in turn makes him tell her that since he trained her, she's a student of his just like Hijikata, Okita, Saito, and the others. It's just a sweet friendship moment that ties her closer to Kondou and the Shinsengumi as a whole.
Hijikata's Route
Chizuru, recognizing how much stress Hijikata is under and desperate to find a way to not be The Load, assumes the Pose of Supplication and begs him to allow her to help. He responds by lifting her chin with his hand, telling her that if she truly wants to help, and isn't asking for selfish reasons, then she shouldn't bow so easily but should proceed with conviction and with her head held high.
As the Shinsengumi captains meet to discuss strategy during the Battle of Toba-Fushimi, Chizuru shows up with rice balls. After promising that she's already taken food around to the men, she persuades them to eat, but Hijikata wraps his up to save for later... correctly judging that Chizuru will not save any for herself. When she objects to taking it from him, they end up splitting it, Hijikata convincing Chizuru to take half by asking who's going to take care of the men if not her.
Saito's Route
There's one moment where Chizuru finds him watching the new snowfall. If you pick the option to ask him if he wants to play in it, she runs over several options before deciding to make him a snow bunny. The resulting CGI is almost too cute to be real.
Chizuru comes down sick while Saito's pretend-defecting to the Guardians. After fading in and out of consciousness, she finds him caring for her. She thinks it's a dream, but when she wakes up the next morning, the bucket he used to cool washcloths is still there. And since everyone thinks he defected for real, this means he basically snuck into the Shinsengumi compound just to look after her.
Heisuke's Route
When Heisuke leaves for the Guardians, Chizuru becomes depressed because they aren't allowed to fraternize. Eventually, Yamazaki and Shimada tell her they need her to go on a special mission which requires her dressing up like a girl. She does, and they bring her to a teahouse, where they ask her to wait before leaving. After a few minutes, she spots Heisuke, who does a double-take when he recognizes her...then sits down, pretends he doesn't know her, and starts chatting. Chizuru then realizes that the whole "mission" was arranged to let her spend time with Heisuke under the guise of gathering intel.
Kazama's Route
At Aizu Castle, Chizuru and Kazama argue over her recklessness in trying to catch up to the Shinsengumi. The fact that he loses his cool out of concern for her life is sweet, but then there's her answer when he points out that the Shinsengumi's legacy is being spat on:
Chizuru: I...I will remember. It doesn't matter if people mischaracterize the Shinsengumi from who they were... I will honor their memory, and you can make damn sure that I'll never forget it.
After that, Chizuru's goals shift; she still wants to catch up to the Shinsengumi, but it's not because she expects to rescue them or have a happy reunion (as most of them have disappeared or died by now). It's because she wants to honor them and their legacy by witnessing their final moments.
When the Shinsengumi surrender, Chizuru asks Kazama if anything he's seen has changed his opinion on humans. He admits that because of his travels with Chizuru, he can understand the Shinsengumi's real characters now—not as foolish lapdogs suffering delusions of grandeur, but as proud warriors who sought to uphold their personal dreams and convictions. He even compares them positively against Demons, which Chizuru thinks is the highest compliment he could have given them.
Throughout the route, Kazama constantly respects Chizuru's agency by running decisions by her. He also recognizes and compliments her strength and sense of responsibility. It's unexpected from him, which makes it all the more touching, with this moment in particular standing out:
Kazama: You know, just because you're no good with a sword doesn't mean you're not fighting. Although your methods are quite different from the Shinsengumi's... You've had your own demons to fight. Even I notice it.
Sannan's Route
Chizuru's admirable in every route, but it's worth noting the heartwarming factor of this route's Chizuru. She worries over the guy who most people can't even get behind. The guy considered unapproachable by most people's standards - the guy who is considered the scariest by the demon commander for his supposedly cold, clinical views and impersonal attitude. And rather than fearing or hating him outright; she gets to know his reasons, gets to see behind the mask, gets to know why he does what he does, and trusts him to do the right thing after realizing he truly does have the Shinsengumi's best interests at heart. She views him with understanding, respect, and eventually love. Her unwavering faith in Sannan is a heartwarming moment, all by itself. It's very telling that this route has an all-around happy ending by Hakuouki-standards despite Sannan usually having very grim ones. Sannan's comment on Chizuru having faith despite everything pretty much summarizes the whole route. It's all about faith. And Sannan was having too little of it for himself, which isn't new for any of the characters, but it's especially notable because even the people around Sannan don't seem to have much of it left for him.
There's something weirdly heartwarming about Sanan's goodbye kiss to Chizuru while she's asleep. Sure, he's gonna leave her - but he probably didn't mean for it to be forever, and he wanted her to know he felt something too. Plus, forehead kisses.
In a rather dark way, the climax of Sanan's route in Shinkai. Sanan has apparently betrayed Chizuru, killed Heisuke, and helped Koudou and Kaoru capture Chizuru. If Chizuru continues to believe in him, then the final battle has Sen and Kimigiku captured by Koudou. Sanan turns on Koudou, Heisuke pulls a Big Damn Heroes, and Sen and Kimigiku reveal they were playing along with their capture. Sanan's reasoning for this? He wanted Koudou to taste betrayal, as Koudou had done to Chizuru.
From the climax, as well: Sannan embracing his want for a happy ending with Chizuru, and dropping this line; "Dreams are worth fighting for. No matter how childish, or improbably they might seem." Aww.
Sannan, seen by some as a stereotypical mad-scientist (which he technically kind of is in some routes), revealing different shades of him does qualify. He has a warmer, more playful side outside of conflicts, and Chizuru remarks on his almost childlike excitement and curiosity at end of the route.
Nagakura's Route
Nagakura offering to help Chizuru with her cleaning in Edo Blossoms, when earlier in the common route, he griped and moaned at the very thought.
where Hijikata becomes sick and everyone does something to try to help him out. Saito picks up medicine despite being sick himself. Okita makes rice porridge. Gen makes sweet bean soup with rice cake (Hijikata's favourite). Heisuke sorts out the paperwork. Ryu brings a citron fruit to cure colds. Kondou wants to do something but everyone else already did it. The best part? Hijikata is smiling throughout the whole interaction with Kondou.