In the second game, second-to-last boss Alice Twilight burns a few pictures before her showdown with Travis. If you somehow take a good look at these pictures, you'll notice she has a husband and son and some form of link with similarly-named Margaret Moonlight.
The Redeemer missile object has "Adios!" scrawled on the side, fitting for a man-portable nuclear cruise missile.
Using console commands to drastically slow down the game speed (very drastically), it's possible to see exactly how the game handles decapitating headshots: the head of the character model simply shrinks down to a dot and a head gib is spawned. Not interesting from any plot perspective, but interesting nonetheless.
TimeSplitters 2 does the same as Unreal Tournament (you can zoom in and see a tiny head using a sniper rifle at point blank). Team Fortress 2 also does it with the Eyelander/Skullcutter's kill animations. Furthermore, you can make a ragdoll in Garry's Mod appear to have no head by simply deflating it until it becomes invisible. This is because it's a lot easier for both the programmer and the computer/console to simply scale vertices or force them all into one point than to actually add to or take away from the 3D mesh.
Halo has these a lot of times on the bullet casings coming out of guns. However, in 2, on Legendary, you can see Jason Jones (Co-Founder of Bungie Studios) wearing only boxers with his hands behind his head, kneeling. What the hell were Bungie doing when that was taken? Wait, don't answer that.
In the ending cinematic of Metal Gear Solid 2 while Snake is talking to Raiden, if you pause at the right point, and zoom into the crowd, a still-living Vamp is clearly visible.
Super Robot Wars loves to do this especially with the ultimate attacks of Banpresto Original major villains.
In Super Robot Wars Z, the enigmatic Asakim Dorwin's Ley Buster attack ends with a Mind Rape that's designed to fuel Wild Mass Guessing. Most of the images that flash across the screen are (probably) merely gothic artwork with meaningless symbolism, but if paused at just the right time, others show possible clues to his past and connection with other characters and plotlines. It doesn't help that he even tells his opponent that he'll show them "my past, my sins, my fate, and my despair".
Super Robot Wars Alpha 3's true final boss Keisar Ephes has an ultimate attack that, if you freeze the animation in certain places (it can be viewed on YouTube), shows the boss standing on a pile of all of the guys you can recruit, as if foreshadowing his victory. Unlike other examples, it's more just for Oh Crap factor.
In Super Smash Bros.. (the original N64 game), the characters have a typical electric damage animation for most of Pikachu's attacks. Many of them showing the skeleton of the attacked character. But, if you attack Samus, and pause in the right frame... you'll see her suitless model, with no clothes at all. She's really well done, but is faceless. This resulted in a Good Bad Bug in which pausing at the right time after hitting her with Ness's PK Thunder would leave her like that.
The ending of Dragon Age II has one. Look at the book Varric and Cassandra are handling at just the right moment and you'll see an illustration of Shale chasing pigeons and another of a woman who looks an awful lot like Morrigan.
Final Fantasy XIII had Siren, who was Boduhm's Fal'cie, almost completely removed from the game, except for one of the flashbacks when Serah tells Snow she's a l'cie.
Even more so for Black Ops, if you can manage to read through the microfiche dossiers before they are redacted. They give you a pretty good backgrounder on all of the characters, and the plot.
Several characters don't get closeups in the intro cutscene of Ultimate Marvel vs. Capcom 3 but are still visible in the background in battling other characters.
In Sonic Unleashed, a Dreamcast with controller is briefly seen just prior to Dr. Eggman firing the Wave Motion Gun to fracture the planet and awaken Dark Gaia. It's in the frames where you get an overhead shot as Eggman has his finger in the air. He also has the Dreamcast in his Egg-o-matic right before Dark Gaia emerges and swats him away.
Just before the Twilight Thorn appears in Kingdom Hearts II, there is a moment when Roxas turns around to see it appear. Just before it cuts to a close up of Roxas, you can see an Organization member, if only for a few frames.
In the Team Fortress 2 official short "Meet the Spy", pause at the beginning scene where it shows the list of alerts. You'll see some pretty funny ones listed.
Extreme slomo videos have revealed that airblasted rockets, which appear to change direction instantly, actually stop and spend a few milliseconds rotating to the desired direction before flying off again.
Some of the Star Bit "constellations" seen in the backgrounds in both Super Mario Galaxy and Super Mario Galaxy 2, which only appear when Mario is traveling from one planet to another. You need to get those Star Bits immediately before Mario finally arrives on the next planet.
In Devil May Cry 3, the intro cutscenes of the stages have the number of the stage hidden on it. Some are fairly obvious (Stage 5's intro fades out on a spray of blood shaped like a 5), some not so much.
All of the characters' info cards in Lollipop Chainsaw. The game displays each one for about two seconds each, so you won't have enough time to read all of the info on them.
In Portal 2, during a later test GLaDOS tells you a supposedly sped-up version of the instructions for that chamber. Slowing it down reveals it to simply be a line from Moby Dick.
In the "Raphael Trailer" for The Stanley Parable, the trailer lists a list of emotions that you can feel throughout the game, including, "Orange", "Being at the Beach", and "Being the Beach".
The giant TV screen outside the Timber TV station, when not in use for the president's broadcast, is covered with a strange rolling pattern of red noise. If you freeze-frame a shot of the TV screen it's possible to make out the text that the "noise" is made up of, lines reading "IAMALIVEHEREBRINGMEBACKTHERE" and "IWILLNEVERLETYOUFORGETABOUTME". These messages are coming from Sorceress Adel, whose imprisonment in an orbital tomb is the source of the radio interference.
During the end FMV sequence, near the end of Squall's epic breakdown/hallucination scene, there's an extremely brief shot of Squall with an empty black void where his face should be.
There's a very minor one in the WildStar Flick "Adventures:" there is a portrait of Ish'mael the Bloodied, the star of "Classes," in the Granok hide-out and he yelps when the door is slammed into his face.