The Gear symbol in Gears of War. There's even a bridge supported by beams stylized to look like gears.
Half-Life's Black Mesa scientific research corporation puts their logo on almost everything. Justified as their complex is a top-secret Elaborate Underground Base and they don't want anything escaping.
Happens again in the sequel, this time, of course, with the Combine logo. The symbol appears on propaganda posters scattered around City 17 and on all Combine equipment.
Kingdom Hearts. The Heartless emblem and the Nobody sigil both show up on pretty much anything connected to their groups. Hell, even that crown design gets around. There's also the classic Mickey Mouse logo, which shows up everywhere in Disney Castle.
One of the pattern options for your gummi ship offers three different sigils to spam at once: the Mickey Mouse symbol, the Kingdom crown, and a keyhole symbol that we might as well call Sora's heraldry and be done with it.
Note that the symbols on the enemies actually do serve a storyline purpose: many Heartless varieties were artificially created, so their symbol was included in order to determine the experiments from the natural "pureblood" variety. The Nobodies all belong to one group and use that mark as a means to identify with it.
Birth by Sleep adds the Unversed logo and reveals that the Heartless and Nobody symbols are both derived from the Mark of Mastery symbol found in the Land of Departure.
Dream Drop Distance adds 3 new ones: Spirit and Nightmare Dream Eater logos (which are very similar to the symbols above) and the Recusant's Sigil, the X used to mark people by Xehanort and the second Organiztion.
Being a Disney property, the series as a whole has a few Hidden Mickeys.
Sonic the Hedgehog's Arch-Enemy Dr. Ivo "Eggman" Robotnik is particularly guilty of this. His logo ("EG" in Sonic the Hedgehog 2 or his face in other games) appears on many of his airships, robots, weapons, missiles, space stations, and even his bedding. Many of his robots are shaped like, or modelled on him in some way too.
Pokémon: The Poké Ball symbol is so iconic that if any player of the games sees an unintentional instance of it, they will automatically make the association.
This sometimes leads one to question the design of Google Chrome's icon, as it looks eerily similar...
Or these lights◊ outside the New York City subway entrances.
They even have the symbol on children's hats. It appears to be considered fashionable in-universe.
The villainous teams all do this with their own logos as well, the most egregious of them being Team Flare, who puts their logo on damn near everything they own.
In Deus Ex, every group in the game puts their logo on every computer system that they own. Even the Illuminati. Also, the MJ12 labs have a gigantic statue of a hand reaching around the globe in the front hall, which makes a very nice backdrop whenever our villains need to foreshadow something.
At least they don't put the logo on stuff that's meant to be shown in public; having your logo pop up on computers inside your secure base guarded by paramilitary types with assault guns makes more sense than plastering it all over the front door.
Additionally, UNATCO is a completely overt agency and Chinese Triads are as overt as it goes for an oriental crime syndicates.
In Mass Effect 2, Cerberus puts their logo in nearly everything they own including their uniforms, ships and facilities, both in their interior and exterior. There are several facilities that have dozens of logos every three feet apart on the walls as though it's some kind of wallpaper pattern. Fridge Logic kicks in when you realize that they are considered terrorists by the Alliance and Citadel Council. You'd think they'd keep a low profile.
The Normandy SR-2 is officially flagged as Cerberus, even, as can be heard in Tali's loyalty mission. And Jack recognises the symbol as Cerberus upon first visual contact (though she has been in and out of Cerberus facilities for most of her life).
This is all the more obvious because in Mass Effect 1 Cerberus did keep a low profile, their operations staffed with troops that looked like regular mercs, and the logo that is attached to Cerberus items obtained by cheat codes is not the same as the one used in Mass Effect 2.
Culminated, of course, with the sigil for Super Smash Bros itself (a circle with two lines crossing in the lower-left quadrant) appearing all over the place in the games (various backgrounds, on crates, the bases of the trophies...).
In Portal, just about every object has the Aperture Science logo on it, from the storage cubes, to the chairs, to the custom computer cases and even tins of beans.
To be fair, they probably made all of that. Which would probably imply that those are not normal beans.
In Perfect Dark, the weapons-manufacturing Megacorp dataDyne likes plastering their "dD" logo on all their architecture (admittedly it is quite a cool logo). Not to mention the fact that the Carrington Institute's logo appears on Joanna Dark's Spy Catsuit (which I'm sure would make her extremely plausibly deniable if she was ever captured!).
In Strife, the Order has many, many images of their Sigil. The Sigil is actually an ancient alien superweapon which you obtain over the course of the game, and you can spamit, but it takes your HP.
While the Halo series was almost an aversion of this trope throughout the Trilogy Halo 3: ODST begins to embody it with widespread use of the various logos for the various corporate, government, and AI entities featured in the game. Particularly those of the Office of Naval Intelligence and the Superintendent. Halo: Reach takes Sigil SpamUp to Eleven with the United Nations Space Command and the Covenant stamping their respective logos on everything from side arms to sand bags.
Command & Conquer: When technology evolved enough to allow use of full rendered 3D graphics for RTS games, Command and Conquer games become fully guilty of this trope. Every unit has at least one logo of its mother faction. Most buildings have symbols as well. It may be justified by the fact that units needs to be easily distinguished - however that is what team colors are for, as the logos are pretty tiny (as the battlefield is viewed from afar), so this justification is pretty weak. Maybe psychological warfare then.
Averted in case of the Scrin, whose logo appear only as a holo-banner making it clear which troops have garrisoned which building.
As an FPS spin-off, thus seeing them from much closer perspective, Renegade takes this up to eleven, with Nod logos everywhere.
And in screenshots of the canceled FPS Tiberium, we can see total GDI logo spam instead.
Nod does this in all its game appearances, their symbol is either a fist, or a scorpions tail. Their barracks has a fist on top of it.
Just Cause 2 has the government of Panau's symbol, a white star on a red background, everywhere. Items include electrical generators, oil tanks, water towers, propaganda trailers, gas stations and vehicles. You can and should destroy anything with that symbol on it in order to increase the "chaos" in the game.
The Yevon symbol (a stylized angel) is everywhere in Final Fantasy X, along with a leitmotif. In fact, the Yevon symbol is on the final boss.
The sigil of the Elder Gods in Mortal Kombat, a stylised Asian dragon that appears in the game's logo, is everywhere. Many stages have it as some form of decoration, even (or especially) when they have nothing to do with the Elder Gods, the Elder Gods themselves take the form of the dragon in the logo, Shao Kahn has it on his hammer, the koins are in the shape of it, and in Mortal Kombat 9, Liu Kang wears it on his belt. Liu Kang also has a recurring fatality in which he transforms into said dragon due to being the champion of the Elder Gods.
In the Fallout: New Vegas DLCs Old World Blues and Lonesome Road you'll often come across a painted version of the Fallout setting's equivalent of the Stars and Stripes. These are done by Ulysses and aside from him leaving his mark also serve a practical purpose: White marks indicate the correct path, red marks indicate dangerous areas and blue markings mean that there's supplies in the following area.
In Dragon Age II, a lot of the architecture in Kirkwall tends to be covered in various Sigils.
As Hawke gets more famous, his/her family logo starts to show up graffitied in places in Kirkwall.
Playstation All Stars Battle Royale represents "All-Star Power" (AP) primarily with a sort of translucent blue energy closely resembling the wavy ribbons seen in every PS3 default background on the main screen. If you look closely, Crosses, Squares, Triangles and Circles can be seen spilling from defeated characters, along with any other large source of All-Star Power. In the final level, Polygon Man's realm is overflowing with these waves of energy, and the four shapes making up the Playstation buttons can be spotted flowing through them in a stream.
Both the Republic and the Sith cover the interiors of their installations with prominent Sigil Spam in the Knights of the Old Republic games. If their ruins are anything to go by, the Infinite Empire of the ancient Rakata was heavily into it as well.
In Mischief Makers, every living creature and inanimate object on Clancer has the same haniwa-like face on it. This includes the planet itself.
Dead Space: All of the containers and at least one location on any given wall, device and all posters will feature the CEC's logo. Given the corporate ownership of the USG Ishimura, it's acceptable.
Dead Space 2 maintains the general feel of the first game with respect to this trope.
In Mirrors Edge, private security firm Pirandello-Kruger is rather fond of a stylized symbol of a guard dog. You can even come across an e-mail from one PK employee to another that refers to it as a "supervillain symbol".
In Back to the Future, the symbol of Citizen Brown's regime in alt-1986 is a human figure with its arms raised, which appears all over the place. When Brown looks at it after his Heel-Face Turn, he gets the idea for the similarly-shaped flux capacitator.