Parental Abandonment/Web Original

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.
In Captain Gamer: Digital Defender, main character Kate Gaines has only had her father mentioned—and that, only as an offhand notice in one paragraph of Backstory!
More than half the protagonists in Lonelygirl15 have parents who are either dead, missing, members of an evil cult, uncaring, or some combination of the above.
That Guy With The Glasses spoofs the Disney's way of doing this in Chester A Bum's review.

Bum: But then he is like "Oh my god, I am a parent and married in a Disney film, I'M DOOMED!" and then he dies.

Occurs quite often in Survival of the Fittest, for various reasons.
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...
This is implied to have happened to at least three of the heroes of The Questport Chronicles, further cementing their statuses as broken cuties.