Given that it's a Visual Novel about The Shinsengumi and the fall of the shogunate, this trope runs rampant throughout most of Hakuouki. Saito and Hijikata's routes in particular are full to the brim with it, both on their own parts and on the parts of Kondou and the subordinates they've inspired to follow them; they are dedicated swordsmen with deeply-held beliefs about what it means to be a warrior, in an age in which swords are quickly becoming obsolete in favor of guns and Western tactics. Their senses of honor also mean that, nearly to a man, the Shinsengumi captains insist on keeping Chizuru with them and protecting her even as they face losing battle after losing battle and everything falls apart around them; whenever it's so much as suggested that it would be better for Chizuru to leave rather than have them risk death to defend her, they bridle at the suggestion that they're not capable of protecting her.
In Soryu Oh's route of Kissed by the Baddest Bidder, Soryu is set for an Arranged Marriage to the daughter of a Triad boss - a marriage which would consolidate their two gangs into a powerful organization which he would be next in line to take over - but declines at the last minute. In doing so, he offends the girl's father and causes him to lose face to the point that the only way for Soryu's gang to smooth things over is to hand Soryu over to be executed. As Soryu is no doubt fully aware of the likely consequences of his decision, his chosen course of action benefits absolutely no one, but he is willing to be executed rather than marry a woman he doesn't love and who doesn't love him when he knows that what he really wants is to be with the protagonist.
Saber in Fate/stay night and Fate/Zero has a pretty bad case of this. She knows her decisions are going to screw her over yet feels bound by her honor and rules of fair play. As an example in FSN, she charges the temple single handed after everyone agrees it's suicide to do so, is commanded not to go and is perfectly aware that at best she will be severely wounded. In FZ, she lets Lancer go assuming that he's going to kill her Master Kiritsugu and therefore remove her from the war. Why? One, she doesn't like Kiritsugu and two, Lancer just helped her out. He only lives because Lancer lives by the same rules.
Naturally, in Fate/stay night, she ends up the Servant of another person who epitomizes this trope, Shirou.
Watase Kasasagi in Root Double: Before Crime * After Days constantly follows this after getting amnesia. Prior to getting it, he's described as assessing every dangerous situation and acting accordingly, which is why his complete 180 baffles his rescue squad co-workers. This leads to plenty of bad ends...half of the time. However, plenty of bad ends have him still apply this shortly after making rational decisions because of his inability to not follow this, with most of the other ones being that the universe is out to get him for using his brain.
Sasami Sasasegawa from Little Busters! is given the chance to rat out the main characters early on in Rin's route for using the sports grounds to practice even though they aren't a real club, and have been hogging the field and stealing practice time from official clubs like the girls' softball club that she's a member of. Instead, she keeps quiet about the main characters' actions. When Riki asks her why she kept quiet about them, she says it's because Rin beat her in their duel from the common route, and she responds by saying that she'll take the field back from the Little Busters by beating Rin in a rematch, rather than ratting them out.