In Borderlands 2 there is a small cave in the Caustic Caverns. It is made of cubic dirt blocks and stone blocks identical to those in Minecraft, and even contains coal, gold, and possibly rare Eridium ore blocks that will drop ammo, money, and Eridium respectively if you break them via melee attack. Enemy Creepers appear here, and they can drop Minecraft-themed cosmetics and weapons.
BoxxyQuest: The Gathering Storm: In the prologue, one of the sailors on the ship hails from Minecraft. Later on, after the shipwreck, you find him on the beach doing exactly what youd expect a lost Minecrafter to be doing: punching a tree to collect wood. He soon runs off to join the other survivors, but in true Minecraft fashion, the top of that tree remains floating in midair for the rest of the game.
An NPC in Crystal Caverns tells the party never to dig straight up or down, which reminds Lance of a mining trip ruined by spiders and exploding monsters.
Later, Whitefall Town has a snow creeper near the weapons shop. Interacting with it with Lance in the first slot causes him to have a Heroic BSoD.
Bullet Heaven 2 reveals that both of the above are because Lance's father was blown up by a creeper, leaving only his shovel, some wood, and a chunk of coal.
One of the mook types in Magicka's "The Stars are Left" DLC are Endermen. They look similar and fight almost similarly too including usage of Teleport Spam... and they will One-Hit Kill your mages if they get into melee range.
Piratez: One researchable tech is literally called Minecraft. It leads to a mining facility, doh.
The Stanley Parable not only references it, but actually drops the player into the world of Minecraft at one point.
Terraria has several Title messages for the bar on top of the window. Chosen at random when the player opens the game or clicks the language button. One of those messages is "Also try Minecraft"
Torchlight II has an area called "Notch's Mine" where the only enemies in there are Creepers that look exactly like those in Minecraft and blow up. There's also a chest inside that contains a random minecraft sword (ranges from Wood to Diamond).
AI: The Somnium Files has ShovelForge, an unapologetic Bland-Name Product of Minecraft that is often played in Let's Play videos hosted by teen idol A-set. You eventually see it for yourself as her Somnium, with Aiba's avatar changed into the familiar Minecraft-style blocky presence to reflect it.
Minecraft became another third-party universe to cross with Super Smash Bros. when Steve, Alex, a Zombie and an Enderman all jointly became the eighth downloadable character (the second offering of the second Fighter Pass) in Super Smash Bros. Ultimate.
An episode of SuperMarioLogan is entitled Jeffy Plays Minecraft!. In this episode, Jeffy plays the titular video game because Mario doesn't want to play with him. When he smashes a lamp with a pickaxe, Mario finds out that he learned it from playing Minecraft, then he pins the blame on the game and gets it banned.
Caillou has a video game called "Dig and Build", which involves collecting resources and building things in a cubic world.
The Rick and Morty episode "The Rickchurian Mortydate" has the duo playing the game. When they stop, Rick says that "South Park did it four years ago" in reference to the aforementioned "Informative Murder Porn" episode. (Incredibly, both "The Rickchurian Mortydate" and "Informative Murder Porn" aired on October 2nd, exactly four years apart.)
An episode of The Simpsons had Bart force Homer to take him to a "Cubecraft" convention.
The South Park episode "Informative Murder Porn" has the kids' parents get addicted to the game.