In the Bount arc of the Bleach anime, Ganju Shiba throws one of his fireworks bombs into the head of a monster made of water and blows it up. Unfortunately, it can easily reform itself and does so. Except the sparks from the firework bomb sizzled out the bottle caps that worked as the water doll's nucleus, killing the monster.
In one episode of Sonic X, Sonic and friends defeat a giant robot by dropping a bomb into its mouth. In the Japanese version, Sonic even exclaims, in Gratuitous English, "IT'S LUNCH TIME!". It's better than it sounds, particularly because the show's opening theme, "Sonic Drive", plays during the sequence.
Shuda in Rave Master can create explosions just about anyplace he wishes. However, when faced with an enemy who causes it to rain on their battlefield (dampening the power of those explosions) Shuda responds by creating one in his enemy's throat.
This is how Homura disposes Charlotte in Puella Magi Madoka Magica. But it's not that obvious for the characters in the scene, since they don't know her true power at the time.
Averted by Matter Eater Lad/Tenzil Kem, who, being from the planet Bismoll, can eat anything, including the raw materials for a bomb, with no ill effects. Unless it's magic.
Issue #4 of the Fantastic Four featured the return of the Sub-Mariner. Namor, in a pique of anger leads a gigantic whale-like creature called Giganto to New York City. After a brief attack the giant creature falls asleep, allowing The Thing to strap an atomic bomb to his back and enter the sleeping beast. The nuke successfully kills the sea monster.
In the film Return to Oz, it's established that chicken eggs are deadly poison to Nomes. At the climax, the Nome King has transformed himself into a giant claymation rock-monster and is dangling Jack Pumpkinhead over his gaping maw. Guess what falls out of Jack's hollow head... the result is more of an implosion, but it's still impressive.
Near the end of Tremors, one of the Graboids is killed by tricking it into swallowing a homemade pipe-bomb with a lit fuse, blowing it to bits. They then try it on the last Graboid, only for it to spit it back at them.
In the sequel, this has become the "standard" solution for killing Graboids: send out a toy remote-controlled car with some dynamite strapped to it ("2 pounds of C4 may be a little... excessive"). When a Graboid snags the car, trigger the detonator remotely from a safe distance. This works quite well, until the Graboids all start hatching out Shriekers.
Chief Brody does this in the Jaws movie. After the shark gets an air tank wedged in its mouth, Brody shoots at it and ruptures it, causing a titanic explosion that blows the shark's head to bits.
Brody: Smile, you son of a bitch!
Busted, unfortunately, by the MythBusters. While you can puncture an air tank, and the jet of air rushing out will make mincemeat out of a shark who has one wedged in its mouth, it's not going to explode unless you have a pyrotechnics team to rig it with remote-detonated C4 beforehand.
Subverted in that it doesn't actually kill the other dragon, just makes it very uncomfortable and provides a good distraction.
Iron Man's solution to this when he has trouble piercing the armor of a Leviathan in the final battle of The Avengers is to let the Leviathan swallow him and then shoot it from the inside. It ends up working, but also damages the Iron Man armor pretty badly.
In the first Critters movie Bradley sees that one of the Crites is about to kill his sister April moments after it had killed her boyfriend, he then tosses it a firecracker it picks it up and eats it, we then see the Crite's stomach inflate from the explosion, it then burps and falls over dead.
In Reign of Fire, the plan to kill the male dragon is to shoot an explosive crossbow bolt into its mouth. Unfortunately, the Genre Savvy dragon destroys the first bolt in flight with a fireball. It then picks up the Villain Ball by patiently waiting for the protagonist to successfully repeat the shot.
There's a similiar Polish folktale about a hero named Krak who builds a rudimentary explosive and feeds it to a dragon that's been terrorizing the land. The Polish people are so grateful they name the city of Krakow after him.
In another version it was Dratewka the shoemaker who killed the dragon, while Krak was already the ruler.
It wasn't exactly IED. According to canonical version it was a lamb stuffed with sulfur. Eating it made dragon drink a lot of water, and eventually burst.
There's also an English folktale (The Mordiford Wyvern) about a man killing a dragon by covering a barrel in spikes and hiding inside it. The dragon swallows the barrel and suffers fatal wounds from the spikes. Of course the man dies too as getting swallowed by and bled on by a dragon is not good for your health.
The Chimera of Greek Mythology was defeated when Bellerophon rammed a big chunk of lead on a stick down its throat, which melted when the chimera tried to breathe fire at the hero.
In Wrath of the Lemming Men (Vol. 3 of the Chronicles of Isambard Smith) Captain smith does this to defeat the Ghast (Giant ant man) Number 8, ramming its own grenade down its throat, and gets his arm bitten off for his troubles. (He gets better.)
In Gateways, a two-headed alligator snapping turtle chomps and swallows anything that moves near her. This proves unwise when Jack fends off her attacks by tossing a grenade.
The Ring of Winter had a hungry monster gobbling up a magical journal. That's basically a Bag of Holding storing attached pages. Which works fine as long as it's not chewed too much — at which point magic fails, immediately and forcibly unloading a cartload worth of paper.
Live Action TV
Used twice in the Star Trek: The Original Series episode "The Doomsday Machine" by first flying a shuttle into the maw of the machine and detonating the engines, having only a small effect. Then flying the wreckage of a starship into the the machine and detonating the impulse engines destroying the machine's insides but leaving the hull intact.
You encounter another in Star Trek Online. The only way to defeat it is by shooting special torpedoes into its mouth - right after it blasts at you.
Subverted in the last season of Stargate SG-1, when Teal'c tried to get rid of the Sangraal's guardian by throwing C-4 into it's mouth. Said guardian was a wyverndragon.
One skit on The Ed Sullivan Show (based on an old IBM training video) was about a Cookie Monster-lookalike taking a machine apart piece-by-piece and eating it. The skit ends with the machine warning the monster that destroying all of the components of said machine will cause it to perform its primary function as the most powerful explosive weapon known to man, as a result the monster combusts.
Goldgoyle deserves special mention, as he had just destroyed both of their Megazords single-handed, and it was clearly a last resort weapon from the Rangers.
As of the Sixth Edition of Warhammer 40000, grenades now have a separate strength-stat that is used when fighting Monstrous Creatures; that's right, even the Mighty Carnifex can be taken down by a unit of humble Tactical Space Marines, all tossing a once-humble (Strength 6) Krak Grenade down its Toughness 6 throat.....
Oddly, in the original The Legend Of Zelda game, it was more effective to let a bomb explode in front of the Dodongo. This stunned it and let you kill it in one shot (and one bomb), while it had to swallow three bombs to kill it that way.
Well the old man did say "Dodongo dislikes smoke."
Pretty much every other boss in The Legend of Zelda: Oracle Games involves Link throwing bombs in its mouth, such as the aforementioned Dodongo, and other bosses like the giant spinning Head Thwomp and the frequent mini-boss Facade.
The Legend Of Zelda Twilight Princess does this too; a giant frog boss in the Lakebed Temple stuns itself when it falls from the ceiling. However, when it opens its mouth, you can toss a bomb in there to stun him again, thus preventing most of its attack pattern.
Before the Lakebed Temple, there are carnivorous plants in the Forest Temple which can only be killed by lobbing Bomblings into them. Similarly, there's a miniboss that's a cross between one of the above plants with a Deku Baba. The plant can only be bombed once the Baba is killed.
It occurs at least once in The Legend of Zelda: Spirit Tracks, with the Fire Babas, fireball-spitting, Link-eating plants that can swallow bombs if you throw them with the proper timing. This kills them in one hit, which is good, since the usual method of fighting them (with your sword), can be quite tedious, and runs the risk of you getting swallowed and taking a fair amount of damage.
Scaldera in The Legend of Zelda: Skyward Sword requires this strategy as well. And, while it's far from the only way to kill them, throwing a bomb at a Deku Baba or Quadro Baba will cause them to instinctively grab it with their mouth, at which point all you have to do is sit back and wait for it to explode.
Several enemies and bosses in the Metroid Prime series require you to morph into a ball, get swallowed, and lay bombs inside the enemy's stomach to damage them. These include the Stone Toad from the very first Prime game and Amorbis from Metroid Prime 2.
A variant occurs in Metroid Prime 3: Corruption. One boss is a huge mining machine with two settings, cutting laser and vacuum. The only way to harm it is to blast some Mook enemies while it's in vacuum mode, so their bodies get sucked inside to jam the laser.
Another variant, also from Prime 3. In one of the deep pits you have to jump into on Phaaze, there's a creature that grabs Samus while she's in Morph Ball form; you have to use the Hyper Ball to kill it (if you don't move to the side to keep it from grabbing you). Weird creature dislikes radioactive lightning.
Now taken Up to Eleven in Metroid: Other M. You have to jump into the mouth of the Metroid Queen and release a Power Bomb in its bowels. A freakingPowerBomb. To put this into perspective, releasing what is acknowledged as the strongest weapon in Samus's extensive arsenal in this way is like taking a nuke and placing it in within a containment field that's been reinforced like hell from the inside-out. And it still ends up trashing the place beyond repair.
A boss from Wario Blast: Featuring Bomberman! runs this way. You have to "feed" it three times, then get out of the way before it gives off an explosion, and only then can you actually deliver a blow that will actually hurt it.
It's not always bombs, though— Psychonauts has the same effect on a boss with boxes of iron nails.
Psychonauts also features Nightmares who can only be defeated by shooting their heads off and throwing one of their own bombs down the resulting neck stump.
Check Calo Nord's journal in Davik's mansion. Calo played it straight, chucking grenades into a rancor's mouth WHILE RIDING ON ITS SHOULDERS. Also, the defeat of the Krayt Dragon on Tatooine parallels this trope, even if it's not QUITE a matter of eating mines.
The Chaos 6 boss from Sonic Adventure tries to suck you into its mouth. You defeat it by getting it to suck in the freeze bombs (Chaos is a sentient, shapeshifting water creature) that Robotnik keeps chucking at you and then smashing it when it freezes; rinse, repeat.
Weldar, the visually impaired welding torch from Banjo-Tooie is defeated by using grenade eggs when he tries to suck the player up. You can also use Fire Eggs, cause hey, he's full of gas.
Andross from the Star Fox series is a well-known example. Firing a bomb in his mouth stuns him briefly, leaving his weak points wide open.
Except in the original, SNES game, where it does...nothing. But since there's no enemies after this point, might as well use your bombs for something visually appealing.
Wart, the antagonist and final boss of Super Mario Bros. 2, can only be killed by Mario, Luigi, Peach, and Toad throwing five vegetables into his mouth.
The Chain Chomp in Super Mario 64 could be stunned by throwing it a Bob-omb on the face.
The Shlurp family of enemies in Super Paper Mario has unlimited defense on the outside so it can only be killed by feeding it a bomb.
In Super Mario Sunshine, King Boo dislikes spicy things, so Mario must stun him by throwing a spicy pepper into his mouth.
The Piranha plants in this game also need to be sprayed in the mouth with water. They always open their mouth for no reason.
In Super Mario Galaxy 2, if Yoshi swallows a Bullet Bill (which he uses to smash open glass cages upon spitting it out) and it stays in his mouth too long, then after a few seconds the Bill will explode and cause both him (and Mario) to take damage.
The only way to kill the sandworms in an early mission of Jedi Academy was to lob a thermal detonator with the timer going on the sand and hope they ate it—the AI and object collision detection made this a bit of a spotty proposition, but they would at least be distracted by it. That's right; they included an enemy even a lightsaber couldn't kill.
The final boss of Pikmin was a lot easier if you fed it bombs like this. The Expys of that boss in Pikmin 2 had a similar weakness, but had to be lured into eating bombs already lying on the ground.
In Metal Gear Solid 2, this is the best strategy for fighting Metal Gear Rays. One missile to the knee will make them shriek with pain, allow a followup shot into their now-open mouth for massive damage.
Metal Gear Solid 3: Snake Eater has this as an extremely easy way of farming gavial meat. Cock a grenade and wait until the gavial yawns. Another very, shall we say, "unique" example in MGS3, where one boss looks for food when he runs low on stamina. By leaving rotten or poisoned food lying around, you can make him vomit to death, for which you are rewarded.
One of the bosses in Aquaria can only be defeated by luring the mooks that he spawn into a gas vent and dragging the resulting gas-bloated explosive mooks into his mouth when he tries a vortex attack.
In Bomberman 64, chucking a bomb into the mouth of the Leviathan boss in Blue Resort nets the player a Gold Card. It also deals twice the damage the bomb would've normally done. This isn't required to defeat the boss, though.
In Gears of War 2, you fight a giant fish who likes to chomp down on your boat. He's defeated by moving into his mouth and chucking grenades into his throat.
In Wario Land Shake It, this is the only way to defeat both the man eating treasure chests in Boogie Mansion and the boss Large Fry in world 5.
Space Quest IV features Roger in a battle with a giant Sea Slug, which he won in the nick of time with an oxygen tank, his clever thinking, and his, uh... cleverness.
The Un'Goro Crater zone has a direct Shout Out to the original Zelda example in the form of a kodo named Dodonga. You don't actually feed it a bomb, though.
Several quests involve feeding bombs to various creatures in order to blow them up — most notably, some worms in Dragonblight, Storm Peaks, and the Molten Front. In some of those, you subsequently collect the tasty meat that is now scattered across the snow.
Time Splitters: The second time you fight 'Princess', 'she' has a propane tank in her mouth.
A boss in House of the Dead 4 is a four-armed zombie with a large tongue. You can deal massive damage to it by throwing grenades in its mouth.
This is actually a common occurrence in any rail-driven gun game, if it has a part that opens, its generally a good idea to shoot at it. Featured most prominently in alien shumps in days of arcade yore, though most players never bother, prefering to just shoot the projectiles and then plug the monster full of lead. For a mechanized version of the trope, the boss of Russia in SNES Super Scope game Battle Clash is nearly invulnerable except on tiny missile pods until he opens his crab-mech's giant 'eyes' which have huge pulse cannons inside. Generally speaking, shooting them in an opening mouth or eye will at the very least stun them for a few frames, or even do additional damage.
U8 in Resident Evil 5 is especially weak to this. Once its limbs are hit enough, its head falls on to the platform after which an input-action to throw a grenade into its mouth (with obligatory cheesy action movie one-liner to boot) and leap out of the way appears. Definitely the easiest way to defeat it.
In Borderlands you can land a critical hit by shooting enemies in a certain weakpoint For Massive Damage in the case of Skag type enemies a critical hit occurs when the player lands an attack when the creatures open their mouth and roar or spit depending on type.
The huge Leviathan boss in Resistance 2 can be harmed by firing rockets into its mouth.
One of the bosses works this way in Fullmetal Alchemist: Broken Angel. Bonus, because you have to transmute said bombs while avoiding attacks. And it heals itself.
Something like this in Kameo: Elements of Power. The demon-tree boss thing can only be killed by throwing enough rocks into its mouth when it's gloating in laughter.
Donkey Kong Country 3 has Belcha, the first boss. He is defeated by throwing beetles when his "mouth" is open.
Nibelsnarf, a giant sand fish/worm/toad thing classified as a Leviathan, from Monster Hunter. One of the easiest ways to deal damage to it is to plant some bombs or Shock Traps and make him chase you into them with its mouth open. Once they go off, it'll stagger him, giving an opening. Another thing is that the most vulnerable part of him is his Uvula.
In Blinx, the best way to kill Keroppers (frog monsters who swallow anything fired at them from the front whole) is to shoot bombs at them.
The player can be vulnerable to this in Super Smash Bros Brawl. Kirby, Dedede, and Wario can each swallow explosive items. While this causes about 5 damage, it's most likely a LOT more preferable to what most explosives do when they go off.
When you're fighting Chub in The Binding Of Isaac, if you put a bomb in front of him while he's charging, he'll eat it and take massive damage when it explodes.
A probable, and often successful, solution to levels in McPixel is to force the stage's bomb down someone's or something's throat. The most common end result is part of their body (head, breasts, butt) will expand to ridiculous proportions and then deflate.
The only way to defeat the Sand Worms in Overlord is to lure blaster beetles over the sands where they live and trick the worms into eating the beetles, causing both to explode.
In Beyond the Canopy, a bloompod monster attacks a Cascadian soldier, eating his water-lance and the fish inside it. The fish then turns itself into fire, explodes the monster, and returns to his owner unharmed.
In Extreme Ghostbusters, one of the villains has the power to break technology, rendering the proton packs liable to explode. So a friendly ghost takes the proton pack bombs and tosses them down the evil ghost's mouth, killing them both.
In the animated Transformers movie, Bumblebee and Spike try to stop Unicron by rigging moon base 2 with explosives which would detonate as Unicron ate the moon. The explosives detonate, and... oh, shit.
A deleted scene from The Little Mermaid that was supposed to happen toward the end of the film, during the wedding of Eric and Vanessa, just right before all of the animals discover that Vanessa is actually Ursula in disguise and attack her, Glut, the shark that attacked Ariel earlier in the film has actually come back to have his revenge. Flounder and Scuttle then immediately dispatch him by tricking Glut into biting into a barrel of gunpowder, causing him to explode.
Double Subverted in the Michel Lah-directed Droopy cartoon "Blackboard Jumble": the Droopies give the protagonist an apple with a burning wick, so he simply pulls the wick out and takes a bite. A second later, the bite explodes, leaving smoke from his ears. He looks dumbfounded at the wick... which explodes too, ashfacing him. Then the apple explodes.
In the Looney Tunes short "Bye, Bye Blackbeard", the title villain is defeated when he is fed some Cartoon Bombs disugised as popovers. He tries to dowse them with some seltzer, but they go off before he can drink.