Given that the titular character's biological family moved to the United Kingdom in the comic's prologue Coming Up Violet one-ups this trope by having an entire substitute family for Ms. Oaks, complete with a mother, father, and two sisters.
In Domain Tnemrot, Dae is like this for Mia, who actually has a father, he just flat out ignores her. Angel is her substitute mother, as her real one is comatose. Despite them having an easy escape from their slavery, they are staying with Mianote Who is their owner because they are literally the only people who care about her. Their plans even include finding a way to bring Mia with them when they do escape.
In El Goonish Shive, Mr. Verres is this for Grace when she moves in with the Verres. Previously Damien was an Abusive Parental Substitute to her and before that Dr. Sciuridae took care of her because she was his Replacement Goldfish though Grace views him as a grandfather. The only real biological parent Grace ever had to care for her was Mr. Guyur (who was killed by Damien) as the other biological parents were either already dead when she was born or non-sapient.
Agatha Heterodyne, the titular Girl Genius, was raised by Adam and Lilith Claynote i.e. Punch and Judy, the Heterodyne Boys' most famous constructs after the supposedly tragic deaths of her parents and the disappearance of her uncle Barry.
Antimony Carver of Gunnerkrigg Court has four substitute fathers. First is her gym teacher, who used to date her mother. Then there's Reynardine, a fox spirit, who was in love with her mother. Coyote is more of a crazy uncle, but he is still protective of her. Oh, and her actual dad should show up eventually.
Ysengrin has (reluctantly) begun entering that category as well, with some wonderful advice (despite his grumpy gruff apparant distaste for the idea)
The original 4 characters of Homestuck have several examples of this, including Dave's older brother and Becquerel, Jade's dog. The subversion is that Dave's brother really is his genetic father through the paradox that is ectobiology, while John's father is actually his half-brother.
Troll society is structured so that most trolls are raised by wildlife, meaning that all of them have a parental substitute, but the most famous example in-universe would be the Dolorosa, who raised the Signless when it became clear that he had no chance of being claimed by a lusus. Her adoptive son would later become a Messianic Archetype.
In Kurami, the titular infant is being raised by her cousin Ana. What happened to Kurami's parents, and why Ana is looking after her instead, is currently unknown.
In Last Res0rt, the powerful Vaeo Family is made up of Vince, his daughter Cypress, and their cousins / nephews Nate and Damien, even though Vince will refer to and treat all three like his children.
Commander: Hey kid, how about from now on before you put anything else in that bag you pretend y' hear your dad's voice in yer head sayin' "Do you really need this?" Jared: My dad never cared about me enough to give me stern fatherly advice like that. Commander: Okay, look't me now, Jared. Do ya really need this? Really?
In Something*Positive, Davan initially believed he might be Rory's biological father, but a DNA test proves otherwise. The real father doesn't step up, though, so Davan becomes Rory's father figure anyway. In strip he admits he wishes he was Rory's father. A Flash Forward to 2020 has one of Rory's friends refer to Davan as "your dad".