I'm a Marvel... and I'm a DC lampshades the frequency of this with comic book characters in its Father's Day special. While recording Father's Day messages, Spider-Man asks if any of the superheroes gathered have parents who are actually alive and gets met with nothing but blank stares.
Trevor James Goodkind (who becomes Phase) starts off in the Whateley Universe as a spoiled rich kid, heir to billions, and second in line to take over all of Goodkind International. But the Goodkinds hate and fear mutants (and his mother is clinically mutophobic). When he manifests as a mutant, he is kicked out of the family, disinherited, and then experimented on by a Mad Scientist in a Goodkind Research lab, some of which activities his parents witness. This may be worse than having your parents die.
There are other examples at the Super Hero School Whateley Academy. Generator has a deceased mother and a child-abuser criminal father. Carmilla's mother is dead and her father is a demon who can't visit this plane of existence under normal conditions. Bladedancer's parents are both dead, her father having been killed by the demon who is pursuing her to this day. There's also Heyoka, Timeless...
In Lovelace One Two, Andi Gannett-Moore has been shuttled from Boarding School to summer camp to summer camp to boarding school continuously since she was a little kid.
Madgie's parents are dead, leaving her in her older sister's, Bunny, care.
On that note, Bunny also cares for Eglantine, Sweetheart and Speckles, Luckie, Binkie, Sorrel, and Magnolia after their mothers abandoned them, though, in the case of Sorrel and Magnolia their mothers died (Magnolia's mother, Margeret, died of illness and Sorrel's mother, Soreene, died in childbirth).
Toki also cares for abandoned or otherwise orphaned children and it is never stated what happened to their parents.
Her twin sister, Doki did adopt a baby that was abandoned right after birth in the hospital that she works in.
Jack Masterson of Chrono Hustle has no idea who his parents are. He grew up in, and occasionally out of the foster system.