In Fairy Tail if you pause at certain scenes you can see strange creatures such as a strange fish/thing/idontevenknow coming out of the water and farting. Some are harder to notice than others.
A lot of crowd scenes in the One Piece anime feature a guy with a panda mask, or a full costume. The Pandaman is never on screen for more than a few seconds, and always hidden like Waldo in a group of other characters.
In Rumiko Takahashi's Fire Tripper (only available on VHS), look very closely at the flames in the early scene where Shukumaru is trying to rescue his little sister Suzu from the burning building. Is that Suzuko, the teen version of Suzu from the future still decked out in her school uniform, standing in the doorway? Why, yes it is, for all of about two frames before the flames cover the shot.
In Super Dimension Fortress Macross, among the buildings destroyed in the first episode are the studios Studio Nue, Artland, and Anime Friend, which worked on Macross. The Studio Nue building has a picture of their chibi-nue mascot on it, and the mascot's facial expression changes to a frightened one while the building collapses. (The mascot is depicted in the lower left corner of the image here.)
Similar to the Macross example above, some of the missiles are sake cans.
The brief scene showing the interior of the Max 5000 mecha reveals that it contains a shishi odoshi.
In one scene where B-ko is in the background, she very briefly takes out some paper fans, waves them around, then puts them away.
In Project A-Ko 2: Plot of the Daitokuji Financial Group, one of the spies shoots a firework rocket which goes out the window and explodes. At the instant it explodes, there's a picture of C-ko waving paper fans.
In the opening of Project A-Ko 3: Cinderella Rhapsody, a split-second before a cut, some of the pool balls split in half.
In episode 10 of Dirty Pair (the TV series), during the aircar chase, Yuri can briefly be seen making the akanbe gesture out the window of the aircar.
In one of the OVA episodes, pausing on the "before-after" slides of Hustle users reveals some additional effects of the drug that are otherwise not alluded to in the episode — for instance, one user's IQ went from 180 to 60.
Ryoga with a word bubble screaming OH MY GOD - because he's looking at Ranma and Akane embracing stark naked.
In the anime it's not uncommon to see characters from Rumiko Takahashi's older works like Urusei Yatsura in a quick crowd shot, or in the case of Cherry the priest, as a statue.
As do early seasons of Sailor Moon. At least once, during a collision (Chibi-Usa landing onto Usagi) there was even a shot of Usagi naked, "sadly" drawn in a Super-Deformed style that prevented any chance of Fanservice. See here (dub episode 109) along with other examples.
Subliminal frames (A filmography term for frames that last well under a second while playing) were often done for slapstick moments in the earlier seasons of the Slayers anime. Some examples include a frame of Zelgadis with a rose in his mouth◊ after Lina kicks him in the first season and a shot of a super-deformed Amelia after she gets hit in the head with a mace in the second.
Ergo Proxy has most of its back story spread throughout the opening credits in this form.
Most of the notes in episode 16 are poems and short stories by Stanley Donwood, a quick search reveals he has a connection with Thom Yorke of Radiohead, who wrote the ending song.
In episode 15 of Cowboy Bebop, there's a scene where the camera follows a car from a side-view perspective. One of the cars going the opposite direction is a yellow Fiat 500, as occasionally featured in Lupin III.
Gundam Wing does this a couple of times. In the episode where Heero is hospitalized, the computer display includes text taken from the readme file for Photoshop's TWAIN plugin. More subtly, when Quatre is shown examining the blueprints to Sandrock, the startup screen includes several technological references to other Gundam series, including the movable frame from Zeta Gundam and the ALICE artificial intelligence from Gundam Sentinel.
When Heero deactivate the nuclear missiles, you can see a sign that says "Intel Outside".
G Gundam does this as well with the last episode or two where various Gundam's from various series help fight in the end. Such Gundams inlcude the original, the Zeta Gundam, and some Wing stuff in there as well to boot.
Which doubles as a Early-Bird Cameo since G is released earlier than W, at least in Japan.
In chronological episode 11 of Haruhi Suzumiya, Mikuru actually has an extremely brief Panty Shot when she jumps over the camera.
Near the beginning of the Fullmetal Alchemistmovie, right after Ed tells Al that he rigged the evil lair to explode, there's a cutaway to show some pipes blowing up. If you pause just before the explosion you see an unflattering drawing of Colonel Mustang on one of the pipes. It's implied that Ed did it.
In another episode of the first anime, "Fullmetal vs. Flame," there's a scene in which Edward and Mustang are fighting. Ed hides in the crowd of military onlookers because Mustang can't possibly blow everyone up for the hell of it. Mustang taunts Ed out with a short remark, which causes Ed to reveal himself in the crowd. Mustang sends a streak of flame that way that blows up the area, sending military men flying everywhere. One man flies directly in front of the camera, moving so fast you barely see him; however, a freeze frame will reveal that he has the most hilarious (blue) face that the artists have ever done in that anime.
He also looks a little like Seiji Mizushima, the director.
Practically every second of every episode of Pani Poni Dash! contains some reference or Shout-Out to something, often unbelievably obscure. The blackboard in particular contains different text every time it's viewed; it's often covered in text, with five or six references at once, and appears for only a split second. The PDF liner notes that come with the Fansub can stretch to over twenty pages.
The show has this to a small degree in the opening, and to a much larger degree during End of Evangelion. End of Evangelion has Misato being blown into pieces and a brief shot of fan mail Anno received, to name only two.
Kaworu's face is shown in a completely red picture, just before we see Rei in moonlight.
Bakemonogatari in general contains countless examples of this trope, thanks to the frequency of "black" and "red scenes," sudden blank frames inserted into the animation which occur when the protagonist blinks or is experiencing considerable emotion. Although they usually don't contain anything other than a few Japanese characters which pertain to the situation, and they probably aren't intended to be read, they sometimes contain important information. In the first episode, for instance, much of the show's background is laid out in this way, but is impossible to read without pausing.
Pokémon: During the first episode of the Club Battle, as we get over a pan of the contestants, Georgia appears twice. Or rather, Georgia appears, and Zorua disguised as her makes a quick cameo.
While we're on the subject of FLCL, it's also worth mentioning an equally-insane effort by one of the directors, Dead Leaves. In a scene where the prisoners get shot, a penis flies off and into another's mouth. It appears around the 17:38 mark, visible in the general area around the robot prisoner's head.
Tiger & Bunny has fun putting in a number of freeze frame bonuses, from informative (Wild Tiger is a former holder of the King of Heroes title, and Mr. Legend was responsible for Jake Martinez's arrest) to amusing (Samantha's photo album included Barnaby's suggestive speedo pics, and someone managed to get an exclusive interview with Lunatic).
Every single time there is text on the screen it is in fully thought out sentences and paragraphs, from the news ticker below Hero TV to the data on a computer screen to the books read.
Episode 5 of Myself ; Yourself has a significant scene involving a tanuki. Two episodes later, a "Tanuki Express" truck zips across the screen.
This trope tells you Rukia of Bleachdoesn't wear a panty◊ underneath her long skirt. This snapshot shows nearly as much of her lower anatomy as is allowed.
Shakugan no Shana - While lasting longer than most examples, in the third episode of season 1 of the anime when Shana trashes various teachers, one of them looks like Adolf Hitler.
Urusei Yatsura has some of these hidden in collision flashes, often in the form of a character's eyes being briefly depicted as large circles with something written inside. It also has some high-speed tracking shots (often used for chase scenes) where various things are briefly visible as the "camera" rapidly moves past them; in episode 158, for example, a shot like this briefly shows Lupin III and Jigen in a yellow Fiat 500.
The beginning of the opening for the Battle Tendency arc of JoJo's Bizarre Adventure shows Joseph's Hermit Purple stand in the background for a split second while he's posing and punching. That's something he'll only get in the next storyline.
Girls und Panzer is full of little details only available when looking like this, such as the correct 'plume' from the muzzle flashes in some of the shots of tanks firing.
Space Battleship Yamato 2199 has a lot of Surprisingly Good English visible in freeze-frames. It also has a massive spoiler hidden in one... at the end of Episode 25, a freeze-frame shot of Dessler's ship exploding reveals that he's cheated death for the third time.
In AKIRA when Tetsuo gets a headache after arguing with Kaneda and starts getting visions, you will see a series of scenes that yet to occur in the film at that point such as Tetsuo's flashback to meeting Kaneda, his mutation, and Tokyo blowing up.
In Lupin III: Dead or Alive, Lupin is shown researching the "sand" he found at Drifting Island. The computer screen briefly gives out the atomic weight and number. The computer Engrish calls it Atomic Quantity, but the numbers are for the weight and number of Gold.
There's also a brief instance in The Pursuit of Harimao's Treasure where, if you pause at just the right moment during the close-up of the boat jump sequence, you'll see a little kid with his hands up the tour guide's skirt, with his hands on her ass!
And in the television special, Albatross: Wings of Death, there's two close-ups of Fujiko's naked fanny as she's running through Lumbach's plane. The first is relatively easy to catch as she runs into the frame, the other is so brief that it almost requires you to pause, then go frame-by-frame in order to see it.