A Boy and His Blob: To defeat the frog-like enemies you must transform Blob into a coconut which will make the enemy eat him. Then call the Blob back, he'll burst out of the enemy, making him explode. Granted, it's a blob, but it's still kind of grisly.
One of the games on the Genesis version of Action 52 was a Frogger clone. Instead of a frog, you played a dog. Get hit by a car, and the dog gets decapitated and his guts pour out.
Little-known PS1 platformer The Adventures of Little Ralph has this in spades, especially near the end. The main character is transformed into a little kid. For most of the game, the deaths are of the simple 'falling over' variety. Then, you get to the Temple stage, where you can get impaled on spikes (complete with blood splatter), crushed by a giant piston (complete with blood splatter), burnt to a crisp, or electrocuted. Even worse is where Ralph falls into a pit of giant maggots, sinking in slowly and disappearing, only to have his skull then pop out, stripped clean of all flesh.
A beta version of the SNES platformer Ardy Lightfoot has Catry, the vulpine boss of the fourth level, sporting a ninja costume (and a slightly more pronounced bustline). On the flip side, her final fate in the bowels of the next level's giant worm is as a half-digested corpse (as opposed to a skeleton in the final Japanese version and just lying prone on the ground in the U.S. version).
The death of Bottles in Banjo-Tooie. It turns out he was inside Banjo's house when gruntilda zapped it with a very powerful energy blast. He exits the house totally incinerated and then falls down the floor, dying when his (visible) soul exits the body. The game is rated E.
Admiral A-Qira's disturbingly realistic death in Battallion Wars II is a bit off-putting, given the game's ambiguously family freindly nature. He gets poisoned by Kaiser Vlad and falls to the ground coughing and retching! I honestly expected him to start vomiting everywhere!
Speaking of cartoony, Brain Dead 13's got a whole mess of death scenes (all followed by resurrection scenes that may not have helped children), and almost all of them that happen to Lance (e.g., getting his limbs, like his hand or his head, cut off; getting drained of blood by a vampiress; getting his spine ripped apart by an atomic wedgie from the Frankenstein's MonsterJerk Jock; getting ripped apart vertically by the eyes; having his soul get sucked out and causing Rapid Aging by ghosts; getting pureed in a blender and then drunk like beer, etc.) are graphic and family-unfriendly. Neither bloody nor gory, but family-unfriendly nonetheless. And just like Super Metroid, this game got a Kids to Adults rating.
In Brave Fencer Musashi, while two of the members of the Goldfish Poop Gang got pretty standard deaths, Topo, arguably the least harmless of the bunch (and of the antagonists period), is the one with the most brutal demise. After a fairly lighthearted game of "Simon Says", she gets brutally shocked by her own stage, screaming in pure agony, and finally spends her last moments painfully writhing and bleeding out. Yeah, the endgame is much darker then the rest of the game.
Death by electrocution or burning in the Dark Castle games, which is accompanied by a bloodcurdling scream.
Miss Peaches in Dog's Life invents a massive machine to turn dogs into cat food. However, the main character is able to turn the tables on her and causes her to fall in the machine by farting in her face. She comes out as an oversized can with her legs sticking out the bottom in a childish Slapstick gag, but then the machine realizes its mistake and pulls her back in! The machine exclaims that she has been "sliced, diced and mashed" and a row of cat food cans are seen exiting the machine.
Some of the boss 'deaths' in the Donkey Kong Country series, but especially in Donkey Kong 64. The most over the top and probably traumatising one has to be after the second Dogadon battle where the dragon flies into the wall with a loud splat, flies up and explodes into light, falls back down in the lava and resurfaces while flailing around on fire and screeching, before sinking back in with smoke rising from it. See at the end of this video
Dragon's Lair II: Time Warp has a pretty revolting ending: After Dirk removes the Death Ring from Princess Daphne, he throws it with a rope at the evil wizard Mordroc, causing him to become a bubbling, fat creature. Seizing upon the opportunity, Dirk slashes the immobilized wizard with his sword, causing him to explode.
The original Frogger was limited to drowning or being flattened by a car/truck, and maybe the occasional alligator. Other games in the series got a little more creative— Frogger 3D (the PS1 and PC game, not the 3DS game) alone had: being mauled by a dog, falling into lava, crushed between spiked walls, getting run over by a lawnmower, and so forth. Frogger 2: Swampy's Revenge also had deaths such as being inflated and popped like a balloon, and getting cut in half, with visible blood. Makes you wonder what the hell the ESRB was thinking when they gave that game an E rating. Then, later 3D games like Frogger's Adventures: The Rescue go back to more cartoonish deaths.
Eric Chahi seems to have a thing for horribly violent death. While this is merely somewhat shocking in games that might plausibly have been for older players, being ripped limb-from-limb by living shadows in the very Disney-esque Heart of Darkness is quite jarring.
And that is just the beginning of the list of horrific deaths the player character can suffer.
Out of This World: Getting bitten by deadly switchblade slugs? Check. Being crisped by the enemy's Frickin' Laser Beams? Check. Scalded to death by steam pipes? Check. Drowning? Check. Mauled by the Shadow Beast? Check.
In Illusion of Gaia, the Jackal's death is quite gruesome, particularly for an SNES game. He has captured the hero's love interest, but the hero plays his flute, activating the booby trap of the room to spew a stream of fire at the Jackal, setting his body completely alight. He slowly burns to death as he tries to crawl his way along the floor to the protagonists before finally collapsing, still in flames. If you exit and re-enter the room afterwards, his bones remain.
Don't forget when Hamlet the Pig jumps into the fire in order to feed the villagers. To eat or not to eat... * sniff*
In "KingdomHearts, several villains suffer horrifying deaths including being burnt to nonexistence whilst having a weapon shoved through the character's chest.
Marx Soul in Kirby Super Star Ultra. After you beat the snot outta him, he blows up... then reappears briefly only to split in half while screaming with an equally horrific facial expression. And then both halves explode and so does the boss arena afterwards. And this is immediately followed by Kirby reigning cheerfully triumphant as the champion of The TrueArena...
In Kirby Super Star, if your Partner gets K Od, it starts to slowly explode, and if there are no enemies to emergency Copy or no health to pick up, they're forced to jump around, flailing as they slowly die. However, this can be prevented by using the Normal Beam, turning them into an item, copying it, and turning your copy back into a partner. But if you've got a Copy of your own, no less a special like Crash, well...
In Kirby's Dreamland 3 there's Zero who, in a final attempt to kill you, rips off its own iris, which is constantly bleeding and after taking enough damage bleeds even more and explodes.
Zero's return in Kirby 64: The Crystal Shards as Zero Two is almost worse when you give it some thought. To push it into the state where you can damage it, you need to repeatedly impale its eye with the Crystal Shards, releasing clouds of blood. This stuns it in pain long enough for you to open fire on its bandaged wound from Dreamland 3, which makes it writhe in agony.
Link's drowning animation is almost as horrifying as Mario's drowning animation in Super Mario 64. When Link drowns, he struggles in the water, sinks, then floats with his back up, dead.
Even though The Legend of Zelda: Ocarina of Time is Rated-E, the death of the third boss, Barinade, is particularly gruesome. Huge boils begin to form all over it's body and it explodes in a burst of green blood and flesh. And none of it disappears after you kill it. Before leaving you can run around the room and see all of the gore splattered on the floor.
Ocarina Of Time really established this as a series tradition for baddies in general and Ganon in particular. The last controllable action in the whole game involves Link slashing at Ganon several times — with the necessary blood flying around — before jamming the Master Sword into his face.
In The Legend of Zelda: Skyward Sword, Ghirahim's death is perhaps the most disturbing one in the entire series. He starts out by inverting the Crucified Hero Shot, being lifted up by the Demon King Demise. Then the hilt of a sword starts to appear from the core in his chest. Demise then pulls it out, while Ghirahim laughs maniacally, almost as if he wanted it to happen. Ghirahim then begins to fade away and is absorbed into Demise's sword. Even if he still seemed to be alive inside the sword, that's only up until the end of the battle, when it dissolves in Demise's hand, completely and instantly.
There are a series of bootleg Lion King games on the NES ported from the SNES. One of them has, as its game over screen, Simba hanging from a noose. And this is supposed to be a port of a "kiddie game"!
The transformed Double literally slicing apart various reploids in Mega Man X4 complete with blood gushing from their wounds for some reason.
The same game has Zero getting Flashback Nightmares of him surrounded by bloodied corpses (his victims when he first awoke as a Maverick), with blood on his hands as well.
Also, early in the game we have Hinawa's death, who was attacked by a Mecha-Drago, a kind of modified dinosaur. The episode seems to have been so violent that one of the reptile's fangs was found embedded in her chest. Probably the coffin was closed during the funeral.
New Super Mario Bros. 1: The first boss is a fight against Bowser, which you win by dropping him into lava, just like in the classic Super Mario Bros....except that back in the NES days, he didn't frantically struggle to escape, fall down into the lava, and briefly resurface as a skeleton after having his flesh burned away. Followed immediately by, depending on who you're playing as, either Mario saying "That's-a so nice!" or Luigi saying "Yay for me, Luigi!" Yeah. That's. Messed. Up.
In Super Mario Sunshine, there are a certain type of enemy known as 'Electro-Koopas', who have electric shells, and attack by flinging their shells like a boomerang at you. How does Mario defeat them? By spraying them with water, so that when their shells come back they get electrocuted. And in a later episode at Pinna Park, Mario defeats a giant one by flipping the grate it was sleeping on, so that it plunges into the water, getting electrocuted also. Wonderful.
Mario's scarily realistic drowning in Super Mario 64. In the DS remake it's changed to a more cartoony drowning. There's also his death by toxic gas, where he grasps his throat and falls to the floor still twitching and possibly alive.
That one scene in Paper Mario: The Thousand-Year Door in which Hooktail eats all the Toads in the audience, and starts chewing them with her mouth open. Sure, there's no blood or gore, but still, seeing numerous Toads getting chewed up while still alive is pretty disturbing. Luckily, you can jump on Hooktail's snout and free a few toads that she gobbled up, but the moment is still freaky. Later on in the fight with Cortez, he eats the audience's souls to heal himself, and you actually get to see the audience members' lifeless husks fall to the floor of the theater and vanish.
This Super Mario RPG fan sequel has a pretty disturbing death and game over scene. Namely, Mario gets shot by firing squad before the game cuts to his funeral with his friends and relatives crying over his corpse in an open top coffin. Cartoony, but certainly a potential way to traumatise any younger Mario fans. here's a video
This trope has been played with as early as Super Mario World in which four Koopaling battles take place over lava. You must push Iggy and Larry into the lava where they are Killed Off Screen. Defeat Lemmy and Wendy and you actually get to see them sink into the lava! It's even worse in the Game Boy Advance remake where it sounds as if they are shrieking in agony!
The EUR/JPN versions of Um Jammer Lammy have a cutscene where Lammy avoids being run over by traffic, but then slips on a banana peel left on the sidewalk by P.J. Berri, lands on the hard concrete, dies, and then finds herself in Hell, which is where Stage 6 begins. Despite this, the game got a 3+ rating in Europe.
However, in the American version, the cutscene was completely re-animated and the level takes place on an exotic island instead, because Sony did not approve of having Hell or the lead character's on-screen death in an E-rated game.
Pikmin and its sequel are surprisingly violent already, being able to carry the carcasses of enemies to reproduce, but the electrocution deaths of some of the Pikmin stand out, being vaporized with visible skeletons. Also the death of the Burrowing Snagret. It simply explodes the first time you defeat it, and then allows you to carry its decapitated head back, eyes open and frozen. The games are rated E for Everyone.
The reason why Psychonauts got a Teen rating, aside from the (mild) swearing, is because in Lungfishopolis you can stomp on the lungfish, with tons of blood spread all around their corpses.
In Sonic Unleashed, Super Sonic flies straight through Dark Gaia's central eye and bursts out of the back of its head. Though you don't see much of that, you DO see Dark Gaia toppling over, crumbling apart with gallons of green blood pouring everywhere.
Space Quest III did this too, with enemies carrying gel guns that would trap you in a solid block of a Jell-O-like substance. Very cartoony! Then Sierra's trademark Have a Nice Death screen pops up, and mentions that there are no air holes.
Not to mention most of the SQ series' deaths were particularly graphic for Sierra standards. SQ 3 alone has Roger suffer a fatal cut to an artery leading him to slowly and painfully bleed to death, not to mention Explosive Decompression or getting half his face blown off.
Or get shredded by a garbage shredder. Or falling to death.
Really, Space Quest was really "nice" about these. The first game opens with Roger being the only crew member still alive aboard the Arcada. Just LOOK at the corpses around the deck. Most were gut-shot and/or bled to death from multiple blaster wounds. There's also the grell, where you're chewed up and swallowed by the creature. Dehydration, Explosive Decompression, having your head dissolve from an acid pool, run over by motorcycles, Body Horror at the hands of the Pukoids...the list goes on.
The original NES game got this. While someone playing the game for the first time might have gotten the impression of a robot exploding to bits during their first playthrough, knowing that there's a human being in that suit turns Samus' death animation into a gory, gravity-obeying splatter.
In Super Metroid, there is one particular boss fight which still seems almost saddening. There a is a boss creature known as Crocomire who, when beaten, falls into the acid below. He repeatedly tries to claw his way out, each time his flesh animated to be melting off of his skeleton, all of the while yelping helplessly in a manner that you might think a dog would as it was dying. Soon, an earthquake occurs, and the bleached walking skeleton of Crocomire appears through a wall, making a last-ditch effort to survive before dropping dead, leaving only the skull behind. Words do it no justice.
Even though the Metroid Prime series is rated Teen, dying in the first is greatly disturbing, and it only gets more so in the "death by Corruption" scene in the third.
Rundas. Most enemies in these sort of games tend to explode or something after they're defeated, but he was impaled by icicles.
The PSN game Super Stardust HD has some enemies that heavily bleed red blood upon being killed. And this is in an E-rated game by the way.
Considering almost nobody ever really died in the previous games in the series, the death of Marquis de Singe in Tales of Monkey Island is kind of shocking. After his immortality elixir fails him, his wounds open up and he gets pushed into his own machine that breaks matter into its particles and spreads them around the seas. The way his scream suddenly cuts off is... unsettling.
Almost immediately after this, and without warning, Guybrush is murdered by LeChuck. Thankfully he gets better.