Beaks and Tentacles

From the more recent He-Man and the Masters of the Universe cartoon, in the final part of the three-episode special "The Beginning" that got the series rolling.

Teela, while trying to get her father out of a giant flying fish ridden by Mer-Man, is assaulted by dozens of angry cephalopods. They don't cause any injuries, but distract Teela long enough for Mer-Man to escape.

These things move lightning fast, which makes it hard to see a lot of interesting details, such as their stalk eyes.

Mantis Tractor

From the movie Coraline

In the seemingly ideal Other World, the Other Father drives a mechanical praying mantis tractor. It spits out seeds and water as it crawls around the garden, and it cuts down plants with it's forelegs, making it a great gardening tool. Although controlled by the Other Father, the mantis tractor appears to be semi-autonomous.

Being a mantis, it could also get rid of pesky aphids.

The mantis tractor also has a rotor than lets it fly into the air. Not sure how often a gardener would need that, but it's always great to have options.

Later on the mantis tractor fuses with a pumpkinized Other Father and a pair of of mechanical, piano-playing hands in an attempt to stop Coraline from retrieving a child ghost's eyes. The Other Father, not wanting to hurt Coraline, broke free long enough to give her the ghost eyes (which where contained within the mantis tractor's gear shift) before plunging the contraption and himself into a pond to their deaths.

The Other World also features insect-themed, semi-autonomous furniture, which take a dark meaning as the Other Mother reveals herself to be an evil spider-like witch.

For those in the know: JERK WAD

Space Pirate Cargo Drone

From Metroid Prime 3: Corruption

Just a minor, non-aggressive labor drone in the Pirate Homeworld. Doesn't attack or anything, rather it spends all it's time lifting and moving some crates around. But it's also carrying something strange...

Hey, what's that above the eyes?

Oh dear, it appears to be someone's head!

This grisly secret is near impossible to see in regular play, as the tiny drones usually stay far from the player, but the game lets you 'scan' most objects to see the it's 3D model (as is being done here) as well as a bit of back story. Of course, the cargo drone's scan doesn't even acknowledge the existence of the strange little head, much less reveal any reason as to why its there. In fact it implies it's just a robot.
Things get even weirder when you look at the Space Pirate Militia model.

A perfect match, but doesn't explain why Pirate heads in the drone. Are they babies being transported? Is it a form of punishment?

Pirate Militia are slaves and criminals within the Space Pirate forces, and are notably thinner. Upon closer examination they look like an eel in a mechanical exoskeleton. Perhaps Pirates are naturally limbless 'eels' and have to rely on mechanical bodies, or perhaps the radioactive element Phazon the Pirates use in vast quantities atrophied their bodies and rebuilt them with machinery, or maybe the Militia Pirates had most of their body parts removed as punishment? Regardless, the Militia don't appear to be hampered in their movements.

Looking back at the cargo drone, the head doesn't appear to be severed (i.e. a beheaded criminal), rather it looks like a full 'eel.' Two prongs hold it in place, and may or may not connect into it's central nervous system allowing it to control the drone. It's still substantially smaller than the Pirate Militia.

Space Pirate tech as a whole is an unsettling mix of mechanical and organic that changes drastically from one game to the next, and the games themselves don't elaborate, so we may never know what's going on here. Perhaps that's intentional.

Goras

The Boss of Star Fox 64's "Titania" level. Apparently just an alien monster, not part of Andross's schemes.

Just look at this poor thing. Droopy eyes, barely any flesh on him (most of which falls off as it takes damage), mouthparts flapping pitifully, looking like some sickly mix of dog and unicorn. I love it.
Despite appearances it's a formidable foe, able to fire lasers and even pull itself back together. The only way to actually harm it is to shoot its barely concealed organs.

I'm not sure what exactly these are. Hearts, maybe?

Goras was only one of a species on Titania. Several skeletons looking near identical to it are littered across the level.

Goras is set to reappear in the 3DS remake with vastly improved graphics, though still as sickly as ever. I daresay he looks even more skeletal and emaciated.

Goras (or another of its species) also appears in the manga Farewell, Beloved Falco, under control of the evil Captain Shears. This Goras is nearly all-green and sports some seemingly artificial tubes sticking out of its head and back, presumably added to control it (or, if its the same one from the game, to revive it).

Freakazoid Transformation

In a clever parody of the classic Wolfman transformation, Dexter shifts between several gruesome faces while changing into Freakazoid in the episode "House of Freakazoid." The individual portraits appear to be painted, a striking contrast from the show's typical animation.

The 5th face is actually Emmitt Nervend. An ongoing easter egg of sorts, the end credits of Season 1 challenge viewers to find the strange little man by telling them how often Emmitt appeared in the episode.

Cafe Aliens

From the Transformers episode "Starscream's Ghost"

There are two different cafeteria scenes in the episode, but both are populated by the same aliens. First we see this odd duo:

First appearing as patrons just standing around not doing anything, later on we see they've become chefs!

This duo ( or another pair of similar aliens) appeared in an earlier episode as prisoners, though they're both white-skinned then:

In the front of the crowd. Also worth mentioning, on of the gray robots in the back appears to lose it's body as it escapes!

Another alien patron, this alien has no apparent mouth, just a tube in its place. Early on it only grumbles, but later on it mistakenly calls a would-be assassin "Waitress!"

I'd question how the tube-mouth alien associated laser guns with food delivery, but soon after this odd fellow eats the weapon. Even though it sparks and smokes in his gut, he enjoys the gun, if thinking it's heavy on the photons.

While purely crowd filler (no lines or even movement) the vaguely fish/lizard-looking alien appears twice, both times seated next to the tube-mouthed thing.

A different pose, wowser!

The Informant

From The Amazing Screw-on Head (quite possibly the greatest thing ever)
Hanging out on a gnarled old tree in the sewers of Marrakesh, the Informant spends his time sending out Morse-coded messages.

The Informant ticks off previous employer Emperor Zombie by telling President Lincoln the last known whereabouts of Zombie's hostage. Zombie sends his vampire minion Patience to rub out the Informant, and she has a rat burn the Informant to a crisp.

Patience also uses the rats for a chair!

Being incinerated isn't the end of the Informant, rather the mummy body was just the host for his true form.

As hinted at by his double-voice, the Informant is actually a pair of scarabs. Fez and monocle wearing scarabs, no less!

The Informant Informants are inadvertently saved from a crushing death by shoe by Screw-On Head himself, who doesn't seem to notice them, and presumably escape.