Rachel from Tower Of God is set up as this, being a childhood friend and mother figure for Baam. The fact that she ran away from their life together should have been a first good hint, but it is subverted when she kills him out of jealousy and fear that he might stop her in her quest.
There is an unusual example in Welcome to the NHK. Misaki Nakahara is a literal Girl Next Door whose innocence and rather plain beauty is, at first, an integral part of her relationship with Satou, combining this trope with Manic Pixie Dream Girl. However, both tropes become subverted when it is revealed that not only does she have many problems of her own, but she has had an unhealthy obsession with Satou for a long time.
Played with in regards to Gwen Stacy of Spider Man. As portrayed in the comics, Gwen was more of an exotic flower whom Peter only met after he left Forest Hill and "went out into the world", i. e. Manhattan and college. She came from an upper-class background, her first boyfriend, Harry, was the son of a millionaire and in her first appearance she was introduced as a high-school beauty queen. However, as she became the Betty to Mary Jane's Veronica, she moved into this.
Shellie from Sin City is sassy but meek enough to qualify.
Mary Jane Watson from the Spider-Man Trilogy movies is an example, arguably due to her being a Composite Character with Liz Allan, who in the comics attended Midtown High together with Peter Parker and Flash Thompson.
He's Just Not That Into You has three: Gigi Phillips is like a basset hound. They're kinda pathetic - so you want to cheer them up. Beth Murphy wants a good man and a husband. Mary is a romantic who has been hiding behind technology.
Mary, the protagonist of the movie Saved, is played as one of these; more importantly, she doesn't lose the general demeanor even after becoming pregnant. This is meant to show Mary as genuinely filled with the Christian spirit of compassion, in order to contrast Mary with her Alpha Bitch rival, who attends the same Christian school environment as her but is hypocritical about being "filled with Christ's love".
Sunshine has the titular character the vampire-slaying, magic-wielding version.
Julie Sims in 1632 is a Girl Next Doorwith a rifle. She's described as being pretty, but not much more, and aside from occasional bouts of angst is fairly level-headed.
Ruby, Ralph's girlfriend in Urn Burial is literally the Girl Next Door; she's lived in the house next door to him since they were born, and whilst not drop dead gorgeous is plenty attractive enough for being familiar and not having any pretensions.
Bernadette (Bernie) Manuelito in the Joe Leaphorn/Jim Chee series of Tony Hillerman is the rare Native American version. She is a pretty, cheerful, down-to-earth fellow Navajo cop who is contrasted to Chee's previous love interest, the beautiful, sophisticated, half-white lawyer Janet Pete from Washington, D.C.
Mary from 7th Heaven starts going out with a neighbor guy who she used to play basketball with. After she breaks up with him he says that playing a game together will help him feel more like they're friends again.
Penny from The Big Bang Theory. She moves into the apartment across the hall in the first episode and that alone gave Leonard some hope that she might become interested in him. She is consistently portrayed as a fairly down-to-earth and friendly girl that helps fill in the gaps with the guys own lacking social skills. Still, as she and Leonard start dating it's made fairly clear that if they weren't neighbors he wouldn't have had much of a shot with her.
To some extent, Alyx from Half-Life. Only debatable thing is that when she was living in Black Mesa, she was only a baby. But then came the Combine occupation and she became a rather hot tomboy by the time Gordon returned two decades later. Since then, they've been together for most of the time.
Note that all three of these girls are royalty (more or less; Lycia's not a monarchy but Lilina's father is nevertheless the head of a country). Then again, the same is true of their love interests, so it's all relative.
In The Fairly Odd Parents, Tootie is a geeky girl who lives near Timmy and quite obviously loves him. Although Timmy at first doesn't return her affections, he sympathizes with her since they both have to deal with Tootie's meaner older sister and Timmy's babysitter, Vicky. According to the Live Action movie Many years later, Tootie returns to town a transformed woman, and Timmy falls in love with her.