An episode of Blossom has Joey talking to God. God offers to turn back time for Joey, who says "I thought only Superman could do that." God's response? "He stole it from me. That's why I killed him." Took place soon after Death of Superman made news.
Dragon Ball Z (which borrowed heavily on the Superman mythos): Goku was killed off at the conclusion of the Cell Saga with the intention of ending the series there and implying a Changing of the Guard. (Executive Meddling resulted in a bringing the character back.)
Shortpacked!: Resident Jerkass Mike makes a joke about the then-recent death of Pope John Paul II, referencing the Reign of the Supermen.
Knightfall, a Batman storyline that was an attempt to replicate the success of the Superman franchise.
The very first issue of Archie Comics' Sonic the Hedgehog, which was heavily comedic, had a Top Ten List with #1 being listed that Sonic "wouldn't be dying anytime soon (but you should still buy multiple copies anyway)" which was represented with a parody of the scene of Lois Lane crying over Superman's dead body with Princess Sally Acorn replacing Lois and Sonic replacing Superman.
Joel: Hey, Hercules, gotta match? Servo: Not since Superman died.
The episode featuring The Creeping Terror has Crow respond with a complaint in a letter about Superman being a "graphic novel" and not a "Comic Book" with "Superman's dead..."
In Supergirlstoryline "Girl Power", the Girl of Steel fights Lex Luthor and directly references her cousin's death, wondering if this'll be "her" Doomsday.
Subverted with "Superman's Dead", a song by Canadian alternative rock group Our Lady Peace: despite the title, vocalist Raine Maida claims it is based on the content television broadcasts to children and what they watch on it - "the dark expectations that are garnered from media images".
In The Angry Video Game Nerd episode "Superman 64 Returns!", the Nerd heads off to the Fortress of Solitude for flying lessons (which doesn't pan out quite well). When he returns, he finds four replacement Nerds made up to look like Superboy, Eradicator, Cyborg Superman and Steel. The Nerd complains about being replaced so quickly before shooing the lookalikes away.