Maya Fey qualifies. While 17-19 isn't old, you wouldn't guess she's that old based on her looks and actions; especially her actions.
Apollo Justice is 22 years old. However, in the second case of the game, the police seem to be under the impression that he's the same age as Trucy (who's 15), shooing him away from the crime scene telling him to "go play somewhere else." Lampshaded in a playable flashback seven years before that, where you can get a picture of Apollo...who looks exactly the same at age 15 as he does at 22.
Likewise, Lamiroir's age is 40 years old according to her profile in the Court Record, despite her looking like a woman in her mid-twenties. Most likely a side-effect of being Apollo's mom.
Phoenix Wright himself in Dual Destinies is 34 years old, but the game recycles his old design when he was in his twenties. Which is amusing because he did look his age in Apollo Justice: Ace Attorney; shaving and an attorney suit seem to make someone look a lot younger.
In Narcissu, the female lead Setsumi is 22 years old, but the 20-year old male lead often comments that she looks considerably younger than him. For Setsumi, whose life consists of a hopeless cycle of hospitalization and release, "time has stood still" ever since she was first hospitalized in middle school.
Angie in Shikkoku No Sharnoth looks and acts like a little girl, but she's about the same age as the both Mary and Charlie and is the only one with an actual fiancee.
Saber is about twenty-five years old (i.e. not counting the centuries since King Arthur's death), but fifteen in appearance (when she stopped physically aging).
Ilya looks about ten years old but is actually older than the seventeen year-old Shirou. The Einzberns modifications to her body made her the perfect Master but also halted her physical growth.
In Fate/Zero, when Ilya is actually around eight years old, Kiritsugu is worried because her growth is so slow that she only weighs about twenty pounds! Even without modifications she wouldn't have matured normally.
And apart from these examples, Gilgamesh drank a youth potion in Fate/hollow ataraxia and is walking around in the form of an adorable elementary school aged version of himself.
Every single female in Kanon, Air, CLANNAD, etc. It's particularly jarring when we're supposed to believe that characters who look no older than sixteen are mothers and aunts of other characters. For example: In Clannad, Akio and Sanae Furukawa look barely older than their daughter, Nagisa. Sanae is often mistaken for Nagisa's older sister in the anime.
Emi is short and has the girliest looks of the main cast, but is one year older than Hisao and the rest of the girls, having taken a year off of school while relearning how to walk.
Shizune's younger brother Hideaki is only two years younger than her (making him sixteen) however the age gap looks even larger.
In Hatoful Boyfriend, Nageki Fujishiro has a zig-zagging example due to bird aging: his human-style portrait is a young-looking boy, which actually fits him as a first-year student, but his bird portrait has the iridescent throat markings and green eyelids of an adult male mourning dove. Further complicating the issue, he's been a first-year student for five years now, and his foster-brother grew up to be one of the teachers.
The protagonist's mother looks younger than he does in Dra Koi apart from her slouch and chain smoking.
The Cure-infectees; their bodies keep aging for five more years until the cells in their bodies have been replaced with infected cells, and then their Super Healing prevents any aging whatsoever. This is why Tsugumi looks no older than 17in either time period.
Strongly implied in Seven Kingdoms: The Princess Problem: Jasper, the personal butler assigned to the Player Character for the duration of the Summit, mentions having taken care of many delegates in the past - despite the fact that the Summit takes place only once every seven years, and Jasper looks far from old. Lampshaded by his character description entry on the game's official website, which lists his age as ???
Yukari from Liar Liar looks young even compared to everyone else. She's short, wears Girlish Pigtails, and her school uniforms are oversized but she's a third year middle schooler in the first game, a high school freshman in the second.
Grisaia no Kajitsu: Makina Irusu looks like, talks like and in general acts like a little girl, even though she is the same age as Sachi. This seems to be genetic, since her mother, Kiyoka Irisu, also looks younger than she really is.
In eden*: They were only two, on the planet., felixes normally stop aging by age 20, even though their actual ages can reach 100, as a result of genetic engineering. In the case of Sion, she stopped aging at an earlier age due to a genetic anomaly.