Death 13 shows an avatar named "Neo001" realize he's in a computer game, before being slain by a player wearing a skin resembling Agent Smith.
Death 21 shows a player finishing off a group of monsters, before Sans comes in and kills the player with giant bone sprites for killing too many monsters. He returns in Death 40 where he kills Stu by slamming him around the room for spoiling the game for Ned.
Death 31 shows a king being slain by a Killer Rabbit for (as the title puts it) stealing all the carrots in Caerbannog.
In Death 32, Ned builds SHODAN from System Shock out of redstone.
In Death 33, "Getting Lost in Nostalgia", the victim is eaten by Pac-Man.
When Sabrina travels back in time in Death 35, she leaves behind a trail of flames like the DeLorean does when it time travels.
Death 36, SnakeTheJaik is doing a stand-up comedy act making fun ofLegolas. Legolas, who's watching this on a computer, reacts angrily and fires an arrow into the distance, which we see kills Jake.
The final death of the episode, "Spliting a Bedrock Block", plays out very similarly to the beginning of Half-Life. The facility that the experiment takes place in is even called "Block Mesa".
Part 3
Death 4, "Living in Kansas" shows Dorothy being sucked up into a tornado.
Death 18 is "Ignoring TLC's Advice" (don't go chasing waterfalls). The victim is Bugs Bunny.
Springtrap appears to jumpscare the viewer in Death 49.
One death has Stu actually eat the Gingerbread Man, similar to how the titular character met his end in the original fairy tale (though here, he's eaten by a human, not a fox).
Death 42 shows a miner breaking into a Skeleton Dungeon, before immediately cutting to a clip from RoboCop (1987), showing the skeletons shooting the player, with the blood censored, of course.
Freddy Krueger also shows up in the main video during Death 7.
Ghostface and Jason appear during Death 9, where Jason kills Ghostface for trying to kill a teenager he called dibs on. Jason appears again for Death 28.
Death 3 shows a military militia dressed up as Mystery Inc.. The actual Scooby Gang shows up in Death 23, where Fred pulls off the head of a crook who glued his mask on, much to the others' horror.
Death 8 shows Norman Bates kill a player in the Bates Hotel. He also appears for Death 29.
Death 10 has Michael Myers appear, slaying one of his victims, before Captain Kirk beams in and shoots him with his phaser for illegally using his image.
Death 29 shows Norman changing the render distance to "Fresh Prince", causing every texture to be replaced with images from the show.
Death 33 and 34 shows Cindy and her husband playing Devil May Cry 3 and then Tetris respectfully, with BlondWolfGirl/PawsterMom and Lil' Timmy imitating the actions in the games, both with hazardous results.
Part 13
In Death 12, MinerMax finds a Super Mushroom while strip mining, making him grow too big for the tunnel he's digging.