The Sandman has a particularly horrible incident in one of the early issues where rogue dreams have converted a still living man into this and draped him all over the walls of his dream-junkie daughter's apartment.
Living Hell can be considered the ultimate Example. The plot of the movie is about a viralcorruption that feeds on energy to grow exponentially. It threatened to engulf the Earth were it not stopped before the sun rose.
In the Pirates of the Caribbean series, many of Davy Jones' crew end up becoming literal parts of the ship, able to talk (sometimes) but not move.
A rare benevolent example occurs in A Fire Upon the Deep; the Old One filled one of the rooms of the Skroderider's ship with this. It turns out to be a complex biotech weapon used to combat the Blight.
The buried tower in The Southern Reach Trilogy, which is made of living tissue. It's able to hide its true nature to a degree and appear as stone to the casual observer, but people who have been "contaminated" by Area X are able to see it as it truly is.
In the Battlestar Galactica reboot, the Cylon Basestar's landing bay Boomer delivers the nuke to (shortly before she shoots Adama) has this look. Justified in that Cylon Basestars of this type are implied to have major biological components, and their fighters are biologically controlled. The inside of their fighters looks like this as well, as seen when Starbuck crawls inside one she shot down in order to pilot it back to the fleet.
In the Helix episode "274," adding growth factor to a petri dish of monkey blood infected with The Virus results in an explosive growth of black biomass that coats and fills a small observation chamber and threatens to shatter it until veterinary pathologist Doreen releases Deadly Gas therein.
White Wolf's firstWorld of Darkness RPG: In Vampire: The Masquerade, many vampires of Clan Tzimisce use their magic fleshforming abilities (flesh and bones, actually) to sculpt humans or other vampires into screaming furniture and living decoration for their lairs, which results in this trope.
In the Tharkold realm of the TORG RPG, Technodemons use alteration magic coupled with their reality's perverse World Laws to produce what they call pain sculptures and pain gardens: living beings melded together, with their responses to pain and pleasure magically reversed. The end result is a writhing mass of gibbering, screaming flesh which gains pleasure from receiving pain and inflicting it on others (including other bits of itself), but agony from doing biologically necessary things such as eating.
Until it was Jossed by Notch, Netherrack in Minecraft was thought to be this, or blood covered stone. It's actually just Red Stone with moss on it.
Many custom texture packs still take that interpretation and run with it.
Prototype has Hives which are buildings covered inside and out in a red biomass. It does in fact serve a purpose: strengthening the Hive by weaving through and around the buildings' walls, to protect the creatures growing inside.
The Shadow from Amnesia: The Dark Descent leaves a tough leather-like mass similar to muscle, that can even pulsate in places. Standing on it for too long hurts Daniel.
The Flood from Halo do this to heavily-infested areas. In the Halo 3 manual it's implied that they do this to collect enough bone matter for the shapeshifting "pure" flood forms that aren't based on an infected body. The effect is usually just a few cocoon-like clumps in the corners, but in Halo 3, we get to see a ship that the Flood has had control over for quite some time, even converting doors into sphincters.
Zerg Creep from Starcraft: Zerg buildings can only be built on the slowly spreading creep and they have an entire building tree of turret-analogues dedicated to spreading it (because both Zerg and Protoss have similar building mechanics, Terrans end up being the oddball race which can put buildings anywhere). It is stated that Creep is used as food for Zerg larva.
The infested Command Centers do play this one straight though.
In-game fluff describes Zerg buildings to be literal organs and Zerg "bases" as whole a literal organism. So creep is somewhat closer to a fluid circulation system - it's required to keep the organs saturated. Infested Terran buildings are somewhat justified in that Zerg cannot manipulate tools, so they need the entire thing hardwired into their command network of telepathic overlords to make any use of it.
Zerg creep is vital to Zerg biology. Minerals and gas are "digested" at the central Zerg organ (Hatchery/Lair/Hive) and then fed to the other organ-buildings in your base through the creep. Without the creep's nourishment, these organs slowly starve and fail. Zerg units can also be fed in this manner - being on creep boosts their metabolism, making them move and regenerate faster. Certain units (like the Queen and the Hydralisk) have their "feet" specially adapted to moving on this creep as well.
In game, when playing as a non-Zerg race, it is usually safe to assume that creep = Zerg territory, and that they can see everything you're doing on while you're on it.
Parasite Eve uses this trope every now and again. It's especially noticeable in post-game content.
Resident Evil 4 has this caused by Las Plagas. Surprisingly, it doesn't show up much in other games.
Doom 3 features a red, meaty growth gradually taking over the base - Sarge even describes it using almost exactly those words.
Phazon from the Metroid Prime trilogy. Phazon is an unusual blue substance with biological properties. It grows like a fungus or plant and the space pirates process it into other solid and liquid forms we see for use in weapons and biological experimentation. It is also hinted to have some form of lower intelligence akin to hive minded single-cells, which in large enough groupings (such as the freaking PLANET made of the stuff) can become sentient.
The DomZ from Beyond Good & Evil mark the things they've taken over with long, dark green tendrils. Everything from machinery to people.
Dead Space - it's growing all over the ship. According to the Apocalyptic Log, the scientists figured it was a 'habitat modifier' - in other words, terraforming.
GOOD NEWS!They're wrong. Bad news: that moss is the dust - that is, shed human skin cells - on the ship being converted by the Necromorph virus.
Breath of Fire IV. You'll eventually come across a false Endless made from Nina's sister. To reach her, you'll have to climb through the bowels (heh), of a building slowly being filled with her presumably still-living flesh, eventually leading to a brief Womb Level.
Dragon Age: Origins features this trope in the Circle of Magi tower as a symptom of the abominations' presence. Red and pink-colored chunks of meat, complete with short spikes, are beginning to cover the pillars and walls of the tower. The corruption gets worse as one goes higher into the tower, and if the music isn't playing, you can hear the squelching noises of the Meat Moss as it grows.
The similarity between this and the corruption of darkspawn is noted by at least one companion.
In Fallout, you find loads of this stuff at the bottom level of the Cathedral's vault. It's part of the Master, who's been mutated by FEV into a Muck Monster.
And also in the original System Shock, though it's justified by it appearing in Beta Grove (simulation of a park, so it has the necessary equipment for plant life). No such justification for the biomass covering much of the interior surface of the bridge module (SHODAN's final stronghold), which is an unhealthy-looking white, like mold or fungus.
Possibly subverted in Resistance, in which you encounter growths that appear to be this. Only for them to explode, revealing themselves as egg sacs full of the game's Goddamn Bats.
Evolva: The towers you have to destroy in several levels? If you watch the initial cutscene, you'll see that the Parasites create them through dilatations from its tentacles. Which means they're made from the same matter as the tentacles.
Warframe has various ships infested with the Technocyte plague, which deforms its victims into horrible, metallic monstrosities. Any ship with the plague present has disgusting patches of slug-like cilia.
The final level in Phantasy Star Online has the player descending into spaceship that was buried in the ground in an attempt to seal away a great evil. As you keep going the metallic walls gradually become more organic until the the whole level feels more like you're walking through a living creature.
Terraria has the Wall of Flesh, a powerful end-game boss. The 1.2 update introduced the Crimson, a variant on the Corruption that replaces the dark-themed monsters with flesh-and-blood themed ones such as the Blood Crawler and the Face Monster.
In Metro 2033, D6's reactor level is absolutely covered in a thick layer of Biomass, which spawns Giant Amoebas and acts as a boss monster.
Evil biomes in Dwarf Fortress can have writhing fleshy 'grass' or blinking eyeballs on stalks in lieu of more traditional ground covering plants. Your livestock will happily graze on it nonetheless, until one of the biome's other hazards destroys everything.
From Welcome to Night Vale: The radio station sound booth in Desert Bluffs is covered, and made out of bloody flesh.
The bottom floors of Project Cadmus in the pilot of Young Justice appear to be made (or covered) in some sort of biological product. It's not quite clear why, since the floor in question also had working (and fully metal) elevators and bank-vault-esque doors, as well as a metal floor in the room for Project Kr. It's possible that it was meant to be an incubator for unborn Genomorphs.
Alien Species Wiki's Habitat Modifier entry.
Several varieties of mold can give walls this kind of look.
Biofilm is basically loads of bacteria that have had a population explosion, and due to the nature of bacteria, are extremely resistant to medicines, as the outer layer absorbs the chemical, dies, gets eaten, and replaced. It usually grows on medical implants and teeth. Fortunately, as of yet, they can't form Combat Tentacles.
Exceptionally thick biofilm, called a microbial mat, covered the bottom of most of the ocean for much if not most of Earth's history (starting fairly soon after the beginning of microbial life 3.7 billion years ago). The mat only disappeared in the Cambrian (about 600 million years ago), when animals learned how to burrow into the sand (which broke up the mat by opening up channels for oxygen to permeate the soil, poisoning the anaerobic bacteria).
Snottites, icky cave formations that are actually bacterial colonies feeding on the mineral water dripping from the ceiling.
The so-called Raleigh Sewer Monster certainly gives off this sort of effect. They're actually large masses of tubifex worms that group together in the absence of natural soil.
And as for why they're pulsating like that, they're photosensitive, so they're recoiling from the massive amounts of brightness and heat from the camera. Poor bastards.