Fairly Oddparents: In season 5 we find out that one of Cosmo and Wanda's previous godchildren was Maryann, who apparently used their magic to assassinate Archduke Ferdinand. Though Wanda's exact word's were that she 'took out' the Archduke, leaving some ambiguity over how much she had to do with his death.  

Hunter The Parenting: Mike Dragons-Wrath is Black Spiral Dancer as well as one of Pentex's highest ranking members. At one point he heavily implies that he was the one killed Swedish Prime Minister Sven Olof Joachim Palme and that he did it because he thought it would be funny. Also from the same series, Big D claims to be the one that ruptured Houdini's appendix instead of Whitehead. Though it should be noted that Big D often lies or pretends to be dumb, so this might not be true in universe.  

Psychonauts: In the mission The Milkman Conspiracy, one of the levels inside Boyd Coopers mind is book depository with a sniper nest, heavily implying that either him or his Milkman sleeper agent personality were involved in the assassination of JFK. 

Watchmen: In the opening sequence, the comedian is seen assassinating JFK.

Umbrella Academy: While this plotline is completely removed from the Netflix adaption, the comics Dallas arc end's with Allison disguising herself as Jacky Kennedy and kills JFK by using her power to make his head explode. 




[Divisive, but still funny, trope] A Real Murder is Attributed to A Fictional Character