In Naruto, pretty much every single character is wearing the symbol of their respective villages due to the fact that they are the equivalent of soldiers. Even the ones who have been exiled or gone permanently AWOL wear defaced ones.
In the Tenchi Muyo! OVAs, Doctor Clay imprints his personal mark on virtually everything he owns. Washu knows this, and is able to locate the bridge of his spaceship because it is right behind said mark on the hull. This is also how she discovers that Ryoko's been replaced by a ShapeshiftingEvil Twin.
Several of the Legendary Warriors including one of the villains have stylized Kanji for their respective Elemental Powers incorporated into their designs. Special mention goes to Takuya, though since all of his Digimon forms except for BurningGreymon have the fire symbol somewhere on their armor.
In an episode of Yu-Gi-Oh!, a milk carton bears the Kaiba Corp logo.
In Fairy Tail, anything a guild owns and all members constantly sport the guild symbol, usually as magic tattoos. Treasure Hunter guilds also have them on their clothing.
In the Grand Finale of We're Alive, it's revealed that 14 years after the initial outbreak the new emerging society of survivors has adopted Ink's symbol that he used to control the zombies as their own. It's on the flag, the armbands worn by guardians and pretty much anywhere else they can put it. The symbol acts as a sort of instinctive stop sign for the infected, preventing them from attacking anything or anyone marked with it so it's widespread use is Justified.
The guilds from the Ravnica block all have their own signets, though how they're placed varies. Gruul signets are illegible territorial markings drawn in what the Gruul Signet card describes as blood, sweat and muck, Simic signets are placed on all their artificial lifeforms as a trademark, Orzhov signets are either carried, indicating a master, or tattooed, indicating a slave. Izzet signets are the most megalomaniacal, as they're frequently redesigned to look more and more like a vanity portrait of the guild leader. The Dimir subvert this, as they are a very secretive guild that officially does not exist So, while they have a signet, it's only seen either by precious few or by those they are about to eliminate.
Any guild-aligned card in Ravnica block (in the guild's combination of colors, in one color with an ability in the other, or using the guild's unique ability) had a transparent version of the guild sigil (except the Izzet card Hypervolt Grasp, which has the Gruul signet by mistake). Likewise, "snow" permanents in Coldsnap had a transparent snow-mana symbol (a snowflake).
Any spell from the Invasion block with a kicker cost had either all or a part of the Invasion symbol on it, depending on the color of mana in said cost.
Also, the Phyrexian symbol and the Mask of Pain (Yawgmoth's symbol) are often used on cards related to Phyrexia. The Mask of Pain appears in the Nemesis logo and was later used as the expansion symbol for Apocalypse.
Speaking of the Invasion block, the Coalition symbol was the symbol for Invasion; parts of it appear in a cycle of cards in Planeshift. Naturally, it also appears on Flagbearer cards.
More recently, the planeswalker symbol is used is planeswalker-related art (but not on the planeswalker cards themselves), as well as in the Magic 2010 logo.
And in Scars of Mirrodin, the cards themselves are getting it: With the exception of the five basic lands and three planeswalkers, every card in the set has either the symbol of the now-native Mirrans, or the before-mentioned Phyrexian symbol (resembling the Greek letter phi Φ) in the background of the textbox. Mirrodin Besieged makes the Phyrexian phi superimposed on the Mirran sun its expansion symbol, and New Phyrexia makes the phi itself the expansion symbol.
Innistrad has the symbol of the archangel Avacyn on nearly every human-related card. It fits better if you imagine it in the place of a Christian cross.
The Koa'ki Meiru monsters from Yu-Gi-Oh! all feature their emblem somewhere on their person.
The Star Wars Customizable Card Game made Rebel and Imperial symbols their card backs, as well as the symbol for characters of that alignment. Lightsabers were used for Jedi/Sith Masters and Force icons.
Most editions of the Illuminati card game by Steve Jackson Games do a variation: The Illuminati symbol (an eye in the pyramid, sometimes simplified to a dot in a triangle) appears on nearly every card, usually hidden.
Oh dear lord, Batman and his obsession with making everything look like a bat.
In the Batman Arkham Series, he sprays his Explosive Gel in the shape of his logo. There is little apparent benefit to this, since most of the things he blows up probably don't need to have a distributed explosion, and in several cases it would actually be counterproductivenote Such as destroying the Titan containers in City.. One possible explanation is that he does it just to amuse himself. note Out of universe, they need "casting time" to keep him from just spamming gel everwhere. Which is presumably why he doesn't just have some sort of remote mine.
His enemies also tend to be, shall we say, "strongly themed" in their choice of accessories, lairs, vehicles... For the Riddler its the question mark.
The two houses of the First have their own respective swirl emblems, and the power-inducing Sigils are the two swirls put together to form a red-and-yellow yin-yang.
Literally inverted by Big Bad Charon when he makes his own "inverse sigil" — the ligis — out of the negative space from the original sigil, and empowers a bunch of test subjects with it.
Lex Luthor is a genius. So why do the killer robots that attack Superman so often have the LexCorp logo on them? (To be fair, he can usually "prove" they were stolen, or their release was a lab technician exceeding his authority, but still...) Possibly justified as it does make the news reports of the robot attacks free advertisement for LexCorp.
Superman's S symbol tends to be used a lot just not to the extent of Bats.
In DC Comics' Atari Force, the Atari "fuji" logo gets incorporated nearly everywhere, especially in the first series. Even the design of the Scanner Onespaceship is a silhouette of the logo.
In Tintin, the symbol of the Bordurian regime is "the whiskers of Kűrvi-Tasch," a stylized representation of the dictator's moustache. It's absolutely all over the country, from flags and official buildings to military rank insignia, hotel lamps and car radiators. This goes as far as written and spoken Bordurian, which uses a circumflex shaped like a curved moustache.
The symbol of Kih-Oskh in The Cigars Of The Pharaoh is used on cigars and the costumes of the members of the secret organisation .
Grant Morrison's Marvel Boy mini-series for Marvel Comics features Hexus the Sentient Corporation, an evil alien "social parasite" that spreads "logo-spores" throughout the atmosphere of its target planet. The spores infect people, forming a corporation which then consumes rival corporations and seduces whole populations through hypnotic ad campaigns, to the point where it literally owns everything and everyone on its host-planet. It then 'brands' the planet with its enormous 'X'-logo and feeds of the planet's resources, leaving behind a dead husk of a world covered in Hexus logos.
New X-Men, another Morrison work, made the X-symbol about as big as possible, while also desaturating the non-X portions of most outfits, making the giant X's stand out all the more. This was to give the X-Men a sort of "brand identity", a topic that Morrison was evidently fascinated by.
A somewhat more realistic version in an early Hellboy story arc, where nearly every piece of equipment from satellite phones and guns to jetpacks goes wrong in the field — and they're all prominently branded with the (fictional) Zinco corporation's logo. While it's not unheard of for things to be obviously branded with logos like that, it's there to draw attention to the CEO's efforts to sabotage the BPRD by taking a loss as the low bidder to force the Bureau into using their sabotaged goods, because he's in bed with Rasputin and the Nazi remnant behind Project Ragna Rok.
An example that doesn't concern organizations but individuals, with the My Little Pony Equestria Girls movies. The main characters, as humans, don't have cutie marks on their skin, naturally, but those symbols of their pony alter-selves can be found everywhere on their possessions: clothes, boots, hair decs, schoolbags, nightwears, musical instruments, laptops, etc. We've only seen Pinkie Pie's bedroom so far in Rainbow Rocks, and unsuprisingly there are balloon motifs on the walls and on her bedcover. (She also seems to have hearts as a secondary motif, like on the pajamas she lends to Twilight.)
Films — Live-Action
In G.I. Joe: The Rise of Cobra, the M.A.R.S. logo is plastered on everything remotely associated with Arms Dealer James McCullen, down to the elevator doors of his secret underwater Arctic base. The killswitch for the nanomite warheads has a screen saver with an animated logo!
In Austin Powers: The Spy Who Shagged Me, Dr. Evil's embossed logo can be found on nearly anything — makeup cases, motorized scooters, record turntables, even the doors of Dr. Evil's secret moon rocket.
Parodied in Spaceballs as part of a Take That against "moichendaising", as everything on the villains' spaceship (Spaceball One) is branded with the Spaceballs logo, down to "Spaceballs the toilet paper" and "Spaceballs the bedsheet." This is largely because George Lucas giving Mel Brooks his blessing to parody Star Wars was contingent on Spaceballs having no merchandise.
In Spy Kids 2: The Island of Lost Dreams, the OSS logo is so ubiquitous that it's a Running Gag.
In the Hitman movie, all of the gear that the super-secret Organization gives its assassins is emblazoned with the group's logo. More than that, all the gear is made with their distinctive design aesthetic, like they're Apple. It's partially justified in the original games, as the fleur-de-lis Agent 47 uses was originally Doctor Ort-Meyer's logo and has no affiliation to 47's current employers, the covert International Contract Agency.
The Hellboy movies feature the BPRD logo on everything, and even has "BRPD" embroidered on their flak jackets. For an organisation so secret that they don't even want people asking "What does BRPD stand for?" This is a carryover from the comics, where the BPRD is more or less openly known.
A more subtle version was done in X-Men. Not so much the logo, but X's were put everywhere they could, particularly the underground doors. Magneto, by contrast, had a lot of "O"s everywhere.
Umbrella was especially guilty of this in Resident Evil: Afterlife. Did Wesker hit the "0" key a couple extra times when he was ordering the static clings or... what? Seriously.
In the Apocalypse film series by Cloud Ten Pictures, the Evil Empire One Nation Earth logo, which is based on the Eye of Providence pyramid design of the Great Seal of the United States, tends to pop up everywhere during the Tribulation.
A bizarre one in Armageddon, where the shuttles are rushed out in order to make the date of the mission — yet feature large decals with their names all over the interior. Apparently the NASA art department fears not the end of the world.
Lampshaded in Tomorrow Never Dies, in which James Bond makes a risky HALO jump into waters that are discovered at the last minute not to be international, but to belong to Vietnam. For obvious political reasons, this causes immediate concern for Bond's CIA contact, who asks if there's any US logos on Bond's equipment. His mood is not improved when the answer turns out to be that it's plastered all over everywhere on him.
Played for laughs in Bloodbath at the House of Death. The mysterious symbol of the evil cult is everywhere in the village... including on the lenses of the blind man's dark glasses.
Even worse is a secret organisation called The Dawn, from a short-lived mid-Nineties series about a "Federal Bio-Crisis Unit". Since their plans to wipe out humanity were so secret, they could be identified by elaborate tattoos on the palm of their hands.
In the classic story "Tomb of the Cybermen", many of the surfaces in the Cybermen's secret lair — including the front door — are emblazoned with a stylized representation of a Cyberman's head.
The Time Lords have the Seal of Rassilon, which the TV Movie took to insane levels.
Firefly: An actual subtle version, as they're never actually mentioned in-'verse, but Blue Sun is omnipresent on every central planet. It also adorns much of Jayne's clothing (including a shirt which River promptly slashes up... while Jayne's wearing it.)
Lady Olenna Tyrell: Another golden rose. How original. I eat from plates stamped with roses. I sleep in sheets embroidered with roses. I have a golden rose painted on my chamber pot, as if that makes it smell any better. Roses are boring, dear.
Heroes: The logo of The Company, half of the famous DNA double-helix, appears repeatedly. It's uncertain if this is Sigil Spam or a Running Gag, however. Word of God says that it has no particular significance to the show's mythology.
Highlander: The Series. The Watchers have the double-layer Masquerade that their organisation is secret, and keeps the target of their watching — the Immortals — secret, too. But they have their logo tattooed on their wrists. Even putting on one's shoulder would be more inconspicuous.
Kings: Butterflies can be seen everywhere in Shiloh and on the uniforms and weaponry of the Gilboan army.
LOST: The Dharma Initiative is probably the epitome of this trope: their logos are found everywhere on the Island. Playing cards, ping-pong balls, chocolate cookies — everything inside their stations has a Dharma logo. It is even present on live sharks! And on random doors embedded in rocks that don't lead anywhere. And on all of the supplies. Except the Apollo bars — those are produced by the Hanso Foundation who also run the Dharma Initiative, so there's no need to alter their packaging.
Mission: Impossible: The episode "The Killer" underlines that it is actually expected of some industries like hotels: When setting up a fake hotel, the good guys are shown applying the hotel's name "Raeburn" in initial miniature on menus and glasses. And they have to do it all in less than 15 minutes because the villain just named the hotel and will soon arrive. He chose one hotel at random but is taken to the bugged one by the second taxi of the line.
MythBusters: Though it is probably more for legal reasons than anything else, this show does this with just about every material they use that isn't going to get blown up/crushed/shot in the next five minutes. They even lampshade it every now and then:
Way back in season 2 of Mighty Morphin' Power Rangers Lord Zedd had a Z on his staff, and his Putty Patrollers had a Z on their chests and knees. The Z on their chests made them break apart like crash test dummies.
The "Zyu 2" episodes of MMPR invoked this with all of the objects pulled out by the Rangers, right down to Billy having a hand mirror with his power coin logo on the back.
The following season, Power Rangers Mystic Force, is at least as bad. The stylized "M" logos are everywhere, incorporated into chestplates, visors... It's even worse if you consider other gear and designs that don't match the logo but are still M-shaped.
Though not the SPD extreme, the dino footprint logo is all over everything in Power Rangers Dino Thunder. Since that was Tommy's power coin symbol as the Green Ranger back in the day, you really gotta wonder what it says about his ego. (Out-of-universe, the connection is a visual version of Lucky Translation: both symbols come from sentai and the connection isn't there.)
Revolution: There is little in the Monroe Republic that Bass Monroe doesn't have his logo on. In the episode "The Children's Crusade", it reaches to horrifying levels in which young people are snatched by the Monroe militia for "re-education" and actually have the logo branded on their right wrists. The episode "Nobody's Fault But Mine" reveals the origins of the logo, by showing that the logo is supposed to represent the friendship between childhood friends Miles and Monroe.
Smallville: By Series 9, Clark Kent took to burning his family crest on the scene of every save he performed, as both a Calling Card and to inspire the disenfranchised population of of Metropolis that they did have someone protecting them.
Stargate SG-1: The Ori use their symbol for everything, their crusaders' weapons, the fire pits they execute nonbelievers in, the power sources in their ships, even their ships themselves follow the pattern.
Star Trek: The Terran Empire put their symbol not only on the uniforms, but also in seemingly every corridor on their 23d-century starships. Compare that to their Federation counterpart across the mirror, who were so frugal about it at the time that it took until the movies to show us what the Federation's symbol actually was.
Although Torchwood One seems to have been far more discreet, as no-one knew they secretly operated out of Canary Wharf. Torchwood Three meanwhile are a small group in Cardiff, apparently operating under the (correct) belief that the Welsh will neither notice or care about all the weird stuff going on all around them, making this something of Refuge in Audacity.
UFO: super secret SHADO puts its name and logo on all of its vehicles, even though SHADO's existence itself is secret.
Pretty much every S.H.I.E.L.D. vehicle in has the organisation's eagle logo on it. The most noticeable is the team's plane, which not only has the logo all over the inside, but has it emblazoned across the upper surface of the plane itself. The inside of every SHIELD facility we see also has liberal applications of the logo, although there is some variation in the level of detail and the style with which the eagle is depicted. Remember, this is a semi-covert agency, and some of these vehicles really shouldn't be emblazoned so openly.
Taken Up to Eleven with HYDRA in the second season; for an organization that's supposed to be completely covert, they don't have any problems wearing HYDRA lapel pins on their HYDRA jackets, carrying precious cargo in HYDRA-branded crates, or painting three-feet-tall logos all over their secret laboratories.
Red Hot Chili Peppers have their asterisk logo, which appears on much of their merchandise, and is identifiable to the band's fans without the name being mentioned. Whenever the band release a new album or single, the asterisk logo will appear in some form on the artwork. Also, many fans show their dedication to the band by having a tattoo of the logo (thanks to former guitarist John Frusciante having one).
The "crossed-hammers" insignia is one of the best-known icons from Pink Floyd's The Wall. The 1980 tours; the movie; the 1990 Berlin show; and the new tours all have this logo emblazoned everywhere.
Naturally, Data East's Batman pinball liberally uses the bat-logo. it even appears on the front of the Flugelheim Museum just because.
The Imperium slaps Aquilas on everything it can, and also seems fond of skulls, whether real or modelled. Individual Space Marine Chapters, particularly the Ultramarines, are fond of this with their Chapter badges; in an image of an Ultramarine from the Deathwatch supplement Rites of Battle there are at least sixteen visible badges on his armour. The Sisters of Battle tend to be covered in Fleur-De-Lys symbols, and the Mechanicus has their cogwheel insignia. In fact, the only imperial institution that avoids Sigil Spam is the Officio Assassinorum, as it'd probably be counter-productive in their case.
Chaos forces, similarly, like to apply the eight-pointed star of Chaos and the icons of the Dark Gods wherever they can, and also use skulls often.
The Tau are almost restrained by comparison, their symbols appear on one shoulder pad of their infantry and the doors of their tanks.
Eldar Aspect Warriors will usually have their Aspect rune painted on their helmets, and then have it molded or painted onto their armor in several places.
And then there's the new Khorne Lord of Skulls◊ kit. Virtually every surface is adorned with either the Blood God's symbol or the eight-pointed star, to the point where each individual section of its treads sports two Khornate skull symbols. The front view depicted in that link has no less than 23 visible Khornate skulls. (Don't even try to count the genuine skulls — even the sculptor lost count.)
The "Unity, Duty, Destiny" symbol crops up everywhere. Every faction uses it, both in and outside of the Matoran Universe. There is a species of burrowing animal that dig all their tunnels in this shape, and even the fragments of the planet Spherus Magna took up this shape when it exploded.
The Mask of Shadows, worn by their leader, is a symbol for the Brotherhood of Makuta that tends to pop up in a lot of places, including a gigantic sculpture of the mask acting as the entrance to his "secret" prison.
The Mask of Shielding is the universal symbol for Physical God Mata Nui, so many places of importance bear its shape, although some are also tributes to actual people who wear the mask.
The smiley face in Lucky Day Forever. Seen in advertising, medals and basically anything to do with the Whites.
The Wulfenbach family signs everything with their rook/castle mark, including tube fasteners and bombs.
This seems to be par for the course for Spark sigils, since Dr. Bettle's beetle, Heterodyne trilobyte and Sturmvoraus winged cog are just as ubiquitous in their respective towns, appearing on everything from candy toffees to eldritch clockwork horrors. Those people love their mad scientist overlords.
Homestuck has plenty of Arc Symbols to go around, but the ones that fit this trope the best would be the Sburb house logo, the Skaia spirograph, the triangular fractal, the Carapacian barcode tattoos, and, on a more sinister note, the Condesce's spoon and fork logos.
In Exterminatus Now, the extremely secret Mobian Inquisition puts their sigil on everything... including a label saying "Property of the Mobian Inquisition" on their secret agent's spy gear.
Jamilla: ...I told them it should say "Not Property of the Mobian Inquisition". Morth: Yes, because that would have fooled me completely.
The monolithic "secret" criminal organization TAROT, from the Global Guardians PBEM Universe, slaps their tarot-card logo on pretty much every piece of equipment their agents use. Rifles, helmets, uniforms, armored assault vehicles, aircraft, radios, gym clothes... even the beer served to the agents in their bases has a TAROT logo on the cans.
Both the Hive Academy and the Teen Titans from the Teen Titans cartoon use this trope.
The Autobot or Decepticon symbols are on every Autobot or Decepticon, often in multiple places. At least this case it's justified for being faction badges. Still kind of odd when the series motto is "Robots In Disguise" and Optimus has a giant Autobot logo on his trailer.
Many items belonging to them will also have the logos.
The Decepticons have a base that's a giant Decepticon symbol. The base even appears in the IDW comics, where the whole disguise thing is emphasized much more than in any other incarnation. In that case, it's fairly justified, as the base is usually only deployed that openly when the Decepticons figure there's nothing anyone can do about them.
Beast Wars even has the Maximal and Predacon symbols in Robo Cam, indicating that our heroes (and villains) are seeing their symbols out of the corner of their eyes 24 hours a day. Lest they forget which side they are on...
The Hanna-BarberaPac-Man cartoon works the iconic "missing pizza slice" shape everywhere in the show's world design, including the sun.
Painting their symbol on everything is apparently an obsession for the ThunderCats, nearly as much as adding the words "thunder" or "cat".
Not to mention the Four themselves, who not only mark their vehicles with their numeric symbol but have a giant holohraphic 4 floating above the Baxter building. The Thing even spray-paints a blue 4 on his chest as a sort of Chest Insignia.
In the second Teenage Mutant Ninja Turtles series, The Foot's tendency to plaster its logo everywhere made for a minor wall banger, as the organization's dragon claw symbol was also used in its legitimate operations, meaning that anyone who got a good look at a Foot Ninja would see the symbol adorning the Foot's very visible skyscraper base and put two and two together without effort.
In Avatar: The Last Airbender, every nation has a symbol but only the fire nation seems to love theirs. It's on all of the military uniforms and vehicles, the nobles work it into their everyday outfits, it's hung just about anywhere in a fire nation city or colony. A container of food can't even be sent to a poor fishing village without stamping it on.
On Wakfu, the city of Breta (especially the palace) isn't just covered everywhere with Governor Cassis' sigil (which, incidentally, features his stylized face), but the town guards also have the habit of stamping everything that enter the city, whether food or people, with said sigil. Including with the big stamp adorning their helmets, which amounts to a solid headbutt. Even Cassis' Humongous Mecha is basically a huge set of stamps, leaving the sigil imbedded into the ground wherever he tries to smash an opponent.
In the Wartime CartoonDer Fuehrer's Face, Swastikas are omnipresent in the satirized version of Nazi Germany. There are Swastikas on all the uniforms of the enforcers, but in addition, the fire hydrants are shaped like Swastikas, the hedges are trimmed as Swastikas, and even the clouds in the sky are in the shape of Swastikas.
If you look closely, you'll see a recurring cyclops triangle symbol throughout Gravity Falls. Though unproven, it may be related to the enigmatic "Demon" Bill Cipher.