In Fullmetal Alchemist, Al likes to store things in his loincloth. Despite the fact that the loincloth is not actually hiding anything due to his... metallic nature, it never fails to freak out the people who see it. They usually tell him to stop doing it, but he seems to like the attention.
As seen in the pic, one of the demons in Wedding Peach pulls a carnival style strength test out of his pants, actually freaking out his devil master by doing so.
The Arrancar Pesh keeps his sword ULTIMAA! down the front of his loincloth, and massively squicksMad Scientist Szayel Aporro Grantz in the process. That's quite an accomplishment, given how disgusting most of what Szayel does is.
Busou Renkin's Papillion has the disturbing tendency to pull whatever item he needs out of his butterfly speedos, ranging from a key to his kakugane to even a second copy of his costume, and of course various copies of his trademark butterfly mask.
Disturbingly, he seems to have had this habit [and the speedo] since before he turned into a humanoid homunculus, as the speedo were under his clothes pre-transformation and the key was clearly in there before the fact as well.
There might be a Shout-Out here to the book and film Papillion, which includes a lot of detail about storing things via an unpleasant method.
In Potemayo, Guchuko can store corncobs, snakes and whatnot in her underwear. She also keeps her battle-axe there when she's not using it.
The titular Mysterious Girlfriend X does this with one or two pairs of scissors, but they're more "holstered" than "hidden" in her underwear (or bikini bottom, if it's summer).
Bulma in Dragon Ball once hid a very large diamond in her panties - leaving no visible bulge, which has made some of the more dirty-minded readers wonder exactly where it was kept. In fact, in the manga, Krillin says he can "tell by the smell where you hid it!"
Which is weird, because he once beat a smelly opponent due to his lack of a nose (though he assumed he could smell Bacterian in the past oddly)
Another (slightly more innocent) version has Krillin saying "It doesn't smell at all" while seeming somewhat surprised. Bulma replies "Why should it?"
In Axis Powers Hetalia, Italy has pulled at least once a pair of boxers... out from his own pair.
Shuichi in the Gravitation manga apparently keeps an important photo Yuki gave him close to, uh, his important member. This causes an awkward moment when Yuki, who wants to fully explain the significance of the photo to him, has to stuff his hand down his pants to retrieve it.
An amateur filmmaker in Planetes, making a movie on a space station without authorization, has all of his equipment confiscated, and has to resort to a backup camera he stored in his pants.
In the first episode of Trigun, the strap on Millie's "stun gun" breaks and it falls on the floor from where it's concealed. She's wearing a very voluminous cloak and later on she's revealed to be wearing a shirt, tie, and slacks underneath, but it's nonetheless a rather alarming sight. Not least because what she terms a "stun gun" is the size of a minigun that fires ammo which appears to have been made on the assumption that the "stun" they were shooting for was "clobber into submission".
In one chapter of Death Note, Mello was depicted stashing his gun down the front of his pants as he left his meeting with Near. This bit (likely understandably) didn't make it into the anime adaptation.
Though the anime team did choose to actually depict just where Light stashed Misa's Death Note when he had to "hold" it. In the manga, it was implied he strapped it to himself with a corset. In the anime, well... 
In Mobile Suit Gundam, a Zeon soldier captured in White Base criticized his captors for not making a proper cavity search before taking out a piece of metal from his mouth and a cord from inside his pants.
In Shin Chan, Nene/Penny several times stores plush animals in her dress, including Happiness Bunny—even a huge pile of them bigger than she is—without any visible indications. This is lampshaded once when her friends told her they could tell by how she walked like she was constipated.
In the first part of "The Tape" story, Hawkeye wound up stuffing his special "Amex Black" card (which has no credit limit) down the front of his pants. While interrogating him Madam Masque is disgusted to hear this and is the only one willing to reach in and get it especially since she's actually Clint's teenage sidekick Kate in disguise.
In Ynyr'sThe Cult of Dionysus, Nymphadora Tonks smuggles prison-escape tools in her "You-Know-What" into Azkaban to spring Harry, Hermione and Luna. She uses her shapeshifting abilities to alter the position of her inner organs to make more room down there (it looked still rather painful). Watching her removing the bag from this orifice gave Harry nightmares til his last day and Hermione vomited from this scene.
Films — Animated
The Emperor's New Groove: Yzma hikes up her skirt, saying "I bet you weren't expecting ... THIS!" Pacha and Kuzco are scared at first ... and then realize she's just pulling out a vicious-looking dagger, and sigh in relief.
In Cloudy with a Chance of Meatballs, Baby Brent sticks the giant ceremonial scissors for the unveiling of Sardineland down the back of his pants. You can even see the handles stick out as he turns around.
In the FernGully sequel, a circus performer pulls a fishing pole out of his pants to save his granddaughter.
At the end of Were Back A Dinosaurs Story, Stubbs the Clown hands in his props when he resigns from Prof. Screweyes' circus, and starts pulling a bunch of random stuff out of his pants. Among the things were a host of traditional pranks like a joy buzzer and a fake Overly-Long Tongue, his backstage pass, his rabbit, the rabbit's back stage pass, "a few birds", a lucky whale tooth which was around his size, and "a giant clam that opens to reveal a mermaid holding the American flag and her normal brother Richard!"
(reaches into waistline as crowd gasps and screams; Bart pulls out paper, they sigh with relief)
(Or was it disappointment?)
Done with a not ridiculously large object in Snatch, but still lampshaded and spoofed. At one point two wannabe gangsters are going to turn over a huge diamond to a mob boss in order to get themselves out of trouble with said mob boss. When they're outside the mobster's headquarters, it turns out that the slightly ditzy one has hidden it in Trouser Space. The Following conversation takes place:
Sol: Well why did you put it down there?
Vince: In case we got mugged.
Sol: You're not from this planet are you, Vincent? Who is gonna mug two black fellas, who're holding pistols, while sitting in a car that's worth less than your shirt?!!
And then right after this, a different gangster who is after the diamond taps on the window of their car with his Desert Eagle. It turns out Trouser Space actually keeps the diamond hidden a little longer.
Bram Stoker's Dracula (1992). Watched by a wide-eyed Mina Harker, Lucy Westenra appears to be reaching into the trousers of her American suitor, saying "Let me touch it; it's so big!" only to remove a huge Bowie knife.
Lampshaded and parodied in Lean on Me, where one high school character imitates the Principal's demeanor while unlocking a door. He reaches into his beltline, finds something, and says "ooh, thats not the key".
The Sting. Johnny Hooker demonstrates trouser space when suggesting that a money courier should hide his money there. This was a trick. During the demonstration, Hooker switched the courier's money for a wad of plain paper.
The Mask: When the Mask is searched by some policemen, they extract all kinds of crazy stuff from his trouser pockets, including a bazooka ("I have a permit for that") and a framed portrait of the lead detective's wife.
In 3 Dev Adam, El Santo never pulls an overly-large object out of his wrestling shorts. However, he does stuff much of Spider-Man's lair into the front of them during his search. Lampshaded in a review by website I-Mockery when El Santo carries around a corpse of Spider-Man, the reviewer comments that El Santo must have ran out of room to stuff him in.
Similarly, In BatmanThe Joker pulls an absurdly long-barreled revolver out of the front of his trousers. It's so long that he shouldn't have been able to walk with that thing down his trouser leg, at least not without a serious limp.
Let's Get Harry (1986). A group of construction workers, financed by a gung-ho businessman and advised by a mercenary, go down to Columbia to rescue a colleague. The mercenary, who's given them strict instructions not to try bringing guns into the country, walks into their hotel room, grabs the businessman by the crotch and says, "I want you to give me this." While the others are gaping at this apparent Ho Yay, the businessman gives a shamefaced grin and produces a 9mm pistol from his underpants.
In Versus, one character (shorter than the others, wearing blue jeans, Yakuza) pulls a gun from trouserspace - specifically, from down the seat of his pants. However, the running gag is that his gun keeps getting taken away from him over the course of the movie - and he keeps pulling additional ones from the same spot.
In the Discworld novels, Nanny Ogg makes a habit of keeping her valuables in her knickers, causing her to turn away and emit all manner of strange twanging noises when she needs to retrieve something.
In Vladimir Mayakovsky's "My Soviet Passport" the character gets a passport out of his trousers. The original poem actually said "out of my wide trouser-legs". The contents of the trousers eventually became a subject for lots of Memetic Mutation in Russia.
Live Action TV
In an episode of The Goodies, Tim is shown to be keeping all manner of things in his boxers, including a wad of cash and a Union Jack tea mug.
A running gag in 'Allo 'Allo! was putting things down people's trousers to hide them. This included sausages, money, and rolled-up valuable paintings.
Also batteries, sticks of dynamite, rolled-up copies of valuable paintings, batteries disguised as sausages, sticks of dynamite disguised as sausages, valuable paintings and copies thereof rolled up and stored inside sausages, the same stored inside baguettes... Are we getting the idea, here?
Gaius Baltar has done this in Battlestar Galactica. Played totally straight, even with a strip search.
Played magnificently in an episode of All That, which featured Baggin' Saggin' Barry, a guy who could pull anything out of his comically oversized pants. When a similarly abilitied rival came into town, he was at first depressed. Then a Magical Negro told him to "reach down deep". The result? A Trouser Space contest with his rival, which he won by pulling out Abraham Lincoln.
His crowning moment came when he missed a flight at the airport because he spent too long failing to get through the metal detector with all that stuff... so he pulled out a plane.
Bill on The Red Green Show is a master of this trope, constantly pulling things out of "storage space" in his overalls, up to and including a whole bicycle.
Bicycle, nothing! One time he retrieved an entire vaulting pole from out of there.
Richie in Bottom fit a whole BBC camera in down there.
There's plenty of space in my trousers... sadly.
The Doctor Who episode, "The Runaway Bride". Donna is forced to hang a lampshade on how The Doctor manages to carry around a large two-handed R/C controller complete with aerial in his trousers.
In the first episode of Wiseguy, The Mafia is surprised to see an Arms Dealer bring his woman to their meeting. As things go badly we see her casually unbuttoning her skirt (how she does this without attracting attention is not explained), then she somehow produces an Ingram MAC-10 and starts blazing away. Now admittedly the MAC-10 is quite small for an SMG, but it's still a large chunk of metal to be hiding between your legs while wearing a tight skirt. It's worth noting that this scene was based on a real-life arms deal in which the narrator noticed the women at the meeting were concealing firearms between their legs just from the way they sat down.
In a season 3 episode of Due South, Fraser manages to smuggle files for Ray out of the police station by hiding them in the front of his trousers.
Ray Kowalski: You're empty handed.
Fraser: Yes, but I am not empty trouser-ed.
Possibly justified, the jodhpurs probably have enough space for it at least.
Late night comedian Craig Ferguson made this trope into a Running Gag on his show, first setting up the joke and then using a robotic sidekick named Geoffrey Peterson to deliver the punchline "In your pants!"
Similarly, "In my pants!" became a running gag of Gilbert Gottfried's for a while on the remade Hollywood Squares.
MST3K - Torgo delivers a pizza to Doctor F. and Frank. He starts to get their complimentary 'crazy bread', reaching into his trousers before they holler "NO!!!"
In an episode of Babylon 5, Sheridan is going to negotiate with a Mad Bomber and wants to keep a com line open with Garibaldi. He knows that his com link will be visible if it's on his hand as usual, and that the bomber will likely think of checking if he hides it in his shirt. So he drops it down his pants. It works great until he sits on it.
Casanova gets an Unsettling Gender-Reveal in more or less this way... when the young man who he was taking to bed appears to remove his own genitals and puts a prosthesis in Giacomo's hand. "Hmm. Mine doesn't do that."
NCIS. Abby, Ziva and Lee have to infiltrate an exclusive nightclub by posing as McGee's groupies. Ziva tells Lee to get a move on and she snaps back, "I don't know where your SIG is, but I'm having trouble walking."
The crew from Hustle pull the same trick from The Sting on a drug dealer at the beginning of the third season.
Since wrestling tights don't have pockets, wrestlers will frequently hide small weapons in the front of their trunks to hide them from the referee. Brass knuckles and bags of "salt" to blind the opponent are the most common, but other things have been done.
Not just weapons, but almost any prop they plan to use. When Chris Masters was doing his "Masterlock Challenge" (offering money to anybody who could break his Finishing Move) he would keep the cash he was offering (and at least once, a plane ticket) in his trunks.
When Chris Benoit stole Kurt Angle's Olympic medals, he kept them in the front of his tights. Partly for how much it annoyed Kurt Angle, partly for security (although Kurt did actually dive in for them once.)
At one point, Eric Young was holding onto an important videotape. In order to prevent someone from stealing it, he once wrestled an entire match with the large VHS tape stuck down the front of his tights (and it was as distractingly odd as it sounds.)
Sting has pulled his metal baseball bat out of his pants at times. It begs the question of how he was able to walk with it in.
Lampshaded in Zork: Grand Inquisitor: From the beginning of the game, the player possesses a "permasuck machine" which is basically a canister vacuum. When he places it on the ground, Dalboz asks, "Just where were you keeping that?"
The original Secret of Monkey Island game. Guybrush Threepwood stores his entire (Significant) inventory in his pants, with a particularly notable example involving the 'Key' to the Monkey-Cave (A gigantic cotton swab)... seeing him pull that out of his pants is vaguely disturbing. In LeChuck's Revenge, he acquires a jacket, and starts storing large objects in his inner pockets instead. Which is a real shame, since he picks up a living monkey at one point, and the sheer number of puns and bad jokes that could've resulted from him stuffing that in his pants would be terrifying.
Don't forget the large dog he's able to shove into his coat.
At one point in LeChuck's Revenge, he finds his entire (usually sizable by that point) inventory has been into a single manila envelope, which he can (and really should) pick up and put in his pants. Upon opening it....
Guybrush: Hey! That tickles.
The storing-stuff-in-his-pants aspect is returned and played up even more in Curse of Monkey Island, especially as you see Guybrush putting everything into and out of his pants. This includes a 60-pound block of tofu at one point in the game.
Don't forget the banana picker Guybrush puts in his pants at one point. And there's a scene in the third game where he's stuck in quicksand: "Hang on, the quicksand is sucking all the cool stuff I found in that snake from my pants. Now THERE'S an odd sensation."
Escape from Monkey Island doesn't animate you taking things out of your pants per se, but if you pull up your inventory in the company of other characters, they will often call you out on the fact that you're technically rifling through your pants (with vaguely naughty jokes thrown in).
A bit subverted in Tales of Monkey Island: Chapters 1 through 4 has Guybrush mention his "trousers" or "pants pockets" when he places items in his inventory; but in Chapter 5, when he places the tiny pyrite parrots into the tip jar he has gotten, he says, "Sorry, guys. I need to keep you in a more contained space than my jacket pockets!"
Played straight in another LucasArts adventure game - The Dig. Somewhat justified in that you're never carrying a great number of objects and none of them are particularly large - your shovel is a pocket shovel - but still beyond what anyone could realistically carry.
And again in Space Quest VI, after trying to pick up a plank:
Narrator: Bet you can't fit that thing in your pants. Guess I was wrong, it does fit. There must be plenty of spare room in there.
Speaking of Sierra, this trope is lampshadedLeisure Suit Larry 2: Looking for Love (In Several Wrong Places) where Larry has to collect a 36-gallon trashcan-sized Grotesque Gulp soda. The narrator wonders how Larry's going to carry it with him...and then remembers that this is an adventure game and lets Larry just stuff the drink in his pocket.
Tex Murphy pulls a 4-foot long bamboo pole out of his in The Pandora Directive.
All of the (bearded) freed prisoners in Metal Slug hide bonuses in their underwear. Including weapons. Is that a Heavy Machine GunRocket LauncherIron LizardFlamethrower Super Grenade in your pocket or are you happy to... Aw, never mind. What makes it hilarious is the giant grin they give you as they shake the bonus out.
The boxers are comically large and he manages to pull them out of his pants in one-piece and then put them back in easily.
Trucy does it with her panties as a magic trick in Apollo Justice: Ace Attorney. Fortunately for the sanity of us all, they aren't panties that she actually wears.
When Johnny Cage wins a round in the original Mortal Kombat, where exactly does he pull his sunglasses from?
Miyamoto Musashi from Sengoku Basara keeps some sort of giant broom/sword/thing don't the front of his trousers, which he pulls out whenever it's time to really kick some butt.
In The Saboteur, Sean Devlin is always seen pulling out his guns somewhere inside his torso or pants.
Lampshaded in ''Thy Dungeonman, who is constantly putting stuff into his "roomy loin-cheese cloth".
Pajama Sam, who seems to have plenty of space in the dropseat of his pajamas.
In The Sims series of games, people pull anything from an engagement ring to garden tools from their pants. Can be made interesting if they are doing that while in their underwear, or naked if you have certain Game Mods installed.
With the Sims 2 inventory system, Sims could pull minivans out of their trousers.
Lampshaded by Barney halfway through Heart Of Evil, when he expresses concern over the fact that Percy might have accidently ejaculated on the Roasted Moose given to him at the beginning of the game.
Later on, Barney himself yells in disgust after he apparently peed himself. It turns out that he had just spilled his glass of applejuice in his underpants. Needless to say, you stock up on the little food you can get during a war.
At the end of Skullmonkeys, Klaymen pulls a potato out of his pants to plug the exhaust pipe of Evil Engine No. 9.
In Darkstalkers, Lord Raptor whips his guitar out of his pants (neck first) for his victory pose.
Our hero, Lee Everett, from The Walking Dead seems to be able to store just about anything he needs in his pants, from the realistic (a pistol) to the downright insane (a blowtorch).
Lampshaded in Luigi's Mansion: Dark Moon. Luigi occasionally needs to take large items (often being half of Luigi's size) back to the Bunker. One time, when you're taking three of them back to a level, E. Gadd chuckles and says "It's a good thing you have such deep pockets in those overalls!"
In the webcomic RPG World, the party's inventory is kept in Hero's pants. This led to an amusing scene when the others had to retrieve items while Hero was unconscious.
In thisOrder of the Stick strip, Belkar says that he concealed his Ring of Jumping somewhere he was "reasonably certain no one would search". Gee, I wonder what finger he's wearing it on?
Light: As for Misa's Death Note, I'll keep it in the only place I know it will be safeómy pants.
Misa: Oh, it'll be safe there! Light doesn't even let me in his pants!
Ryuk: You're not missing anything.
Joker in Batman: The Brave and the Bold once decided against the gas gun, knife, or pie he had up his sleeve and instead went for the bazooka that came out of his pants.
An episode of The Fairly OddParents had Francis the Bully shoplifting and sticking increasingly enormous items into his pants, including a large-screen TV, a generator, a car tire, and a 55 gallon drum.
One episode of Total Drama Island features Cody somehow storing a loaf of bread and a can of soda in his pants without any apparent difficulty walking.
Cody: I was gonna make us a...romantic picnic.
Gwen: With bread from your pants?!
The dragons in Dragon Tales have pouches that they can store seemingly anything in. They don't wear pants, but it's close.
Insane in the Mainframe: While thinking he is a robot, Fry takes some sandwiches from his pants and offers them to his friends, saying he took them from his compartment. They are not interested.
The Bird-Bot of Ice-catraz: The nature hippie encourages the use of the butt for handwarming (and implied for storage), since it's "nature's pocket".
Mother's Day: Professor Farnsworth keeps the controls for his albino shouting gorillas down the front of his pants, as a Spear Counterpart to how Mom keeps the Universal Robot Controller in her bra.
Animaniacs's Yakko keeps lots of things in his pants. Wakko would count if he wore pants.
He does keep Baloney in his Slacks...
A running gag in Looney Tunes is that often characters will pull anything they need out of their pants - most commonly binoculars.
In The Simpsons episode "You Only Move Twice", Scorpio hands Homer some un-packaged sugar from his pants pocket. He then offers cream to which Homer quickly refuses.
Histeria! has Mr. Smartypants, and the segment of the show "What's in my pants" which usually always caused the Network Censor an ulcer.
In an episode of She-Ra: Princess of Power, her brother He-Man pulls out an absurdly long grappling hook from his furry, extremely short tights. It was long enough for She-Ra to hook it onto a space ship, while it was in space, from the surface of her planet. Try not to let Fridge Logic set in, it will be too painful.
On Rugrats, Tommy often pulls stuff out of his diaper, usually his trusty toy screwdriver. Phil and Lil have been known to keep stuff there, too, such as god-knows-how-old graham crackers. Which makes one wonder, how often do the parents change the kids diapers if they never know they have all this stuff in them?
In Fantastic Max, Max often pulls stuff out of his diaper. AB even comments about how unsanitary of a habit it is considering Max uses the object he pulls out to his fullest advantage.
In Ed, Edd n Eddy, whenever Kevin needs his bike he pulls it right out of his pants.
Razor Ramon Hard Gay himself was once filmed visiting Harajuku to demand that the punk kids there do the right thing and call their dads on Father's Day...using a cell phone he drew suggestively from the front of his leather hotpants.
ZP Theart, former lead singer of DragonForce, tends to stuff his wireless microphone down the front of his pants whenever he needs his hands free onstage.
There is a video on youtube (believed to be a "warning video" to highlight the dangers of letting teenagers wear baggy pants) that shows a teenager pulling an absolutely improbable amount of guns and knives out of his pants... including a full-size shotgun.
It first achieved notoriety when it was shown in Bowling for Columbine, long before jeans went from baggy to skinny (Fashion Marches On?)
A notorious design of some school uniforms in Australia included a change purse in the front of the shorts ON THE INSIDE and no other pockets.
Jennifer McCarthy was arrested after threatening her boyfriend with a pistol she pulled from a very specific place. A place you could only reasonably hide a weapon while wearing only lingerie.