Natsuhi Ushiromiya tries her hardest to play this trope straight. It helps that she has the looks, comes from a traditional family of Shinto priests and is very dedicated to her husband, but she ultimately has too much of a Hair-Trigger Temper to truly be a yamato nadeshiko due to the constant stress the family she married into puts on her.
Nagisa Furukawa and her mother Sanae. Sanae-san's main flaws as a yamato nadeshiko is that she tends to be a Cordon Bleugh Chef when it comes to making bread and that, in the anime series, she becomes a Stepford Smiler who doesn't allow herself to grieve for the dead Nagisa in the name of raising Nagisa and Tomoya's daughter Ushio as best as possible. Nagisa is more of a Shrinking Violet, but slowly evolves into one and it shows VERY well when she gives a VERY scaringly stressed Tomoya a rather fierce Cooldown Hug to calm him down. Kikuko Inoue count: 17
Mei Sunohara, the kid sister of Tomoya's friend Youhei, is a yamato nadeshiko crossed with Cheerful Child. Whenever she visits Youhei, the first thing she does is clean his (truly filthy) room.
Kotomi Ichinose is one crossed with a Teen Genius, despite her eccentricities. Her traits become more obvious as she befriends the rest of the gang. In ~After Story~ she shows up to the New Year's party in a kimono, the only girl to do so in the scene. She also has the calm, unassuming nature and domestic abilities to qualify, and a seiyuu to match. On the other hand, what she fails to do properly is music - her violin is a memetic weapon more than anything.
Uraha in Air: Though it isn't explicitly stated, she invokes and parodies this trope on purpose. Kikuko Inoue count: 18
Fate/stay night: Sakura Matou. When she grew interested in Shirou, she resolved to reform herself to be more appealing. This is why she spends so much time cooking for him. Her gentle and quiet demeanor also strikes a contrast with other love interests like Rin and Saber. It turns out that she's actually a Broken Bird and Stepford Smiler who's been through a massive Break the Cutie process ever since she was a kid, at the hands of her adoptive family: her YN traits were born from both her desire to be more appealing to Shirou and as a psychological defense. So when she snaps in her own route... SNAP she does.
Ace Attorney: Iris is kind Raven Hair Ivory Skin Beauty, who is always polite to everyone. She also very protective of people she cares about as shown when she gently, but firmly cut of Phoenix arguing with Edgeworth, when they were on a way to rescue her cousin, or when she claims she'd do anything to stop Dahlia from killing Phoenix, including killing her, had she known about her plans.