In Yu-Gi-Oh! ZEXAL, Housaku Yasai uses move a called "Tomato Matryoshka" which allows him to summon another "Tomato Matryoshka" from his hand or deck when it is Normal Summoned.
Tengen Toppa Gurren Lagann. The titular mech is the size of a galaxy, piloted by Choginga Gurren Lagann, the size of a moon, piloted by Arc Gurren Lagann, the size of a mountain, piloted by Gurren Lagann, the size of a house, piloted by Simon, the size of a man. Simon pilots himself.
Turned Up to Eleven in the movie edition, where the titular mech pilots Super TTGL, which is the size of several galaxies (TTGL makes up about the size of Super TTGL's head).
In Axis Powers Hetalia, Santa went missing one year, so the nations helped by delivering presents themselves. Japan filled his gifts with games and boxes nested inside larger boxes.
Kid: (opening his presents) "Whoa! More boxes are in this box! No matter how many boxes I open, there're more inside them, Dad! It's like a matroyska doll!"
Used in the Wowser episode "Slap Happy Birthday" when Wowser finds a birthday present from Ratso on his doorstep, which turns out to be one of these, only for Wowser to find an itty-bitty (explosive) bone after taking all of the boxes out of the other.
In a The Fabulous Furry Freak Brothers comic, Fat Freddy brought home a shrink-wrapped package of marijuana. It had another layer of shrink wrap inside, which had another layer, which had another... although just before Franklin and Phineas would have killed him for spending their drug money on plastic bags, there was indeed a tightly compressed bag of marijuana at the very center.
A Mr. Hyde character that keeps a smaller Hyde under his hat, who in turn has a smaller Hyde under his hat.
A nested doll appears in the "Making Christmas" sequence, the smallest doll of which contains a live scorpion (We never see it opened).
In Ice Age: A Mammoth Christmas, Scrat gets a giant acorn from Santa, which opens up to reveal another acorn inside, and another, and another and another, until eventually he gets the real (small) acorn in the middle.
The closing credits of Cars 2 showed Fillmore, Sarge, Luigi, and Guido as nesting dolls.
In Rise Of The Guardians, Badass Santa Nicholas St. North challenges Jack Frost by asking, "What is your center?" He uses a Matryoshka doll of himself to illustrate his point. Each consecutive shell reveals a facet of his personality; powerful, jolly, mysterious, until he shows the center doll, which has a baby-face with wide eyes to illustrate his center, his sense of wonder.
Inverted in The 500 Hats of Bartholomew Cubbins (also by Dr. Seuss): Cubbins' hat contains an identical hat. Removing the second hat reveals a third hat, which also looks exactly the same. At hat 451, the hats actually start to get bigger.
In Cory Doctorow's Someone Comes to Town, Someone Leaves Town, 3 of the protagonist's brothers are Matryoshka dolls in the literal sence (by the way, his father is a mountain, his mother a washing machine and two of his other brothers are an island and an undead ghoulish thing), so when the one with the actual digestive system goes missing, the other 2 start to starve.
In The Third Policeman, one of the policemen occupies his time making boxes which contain perfect smaller replicas of themselves. The protagonist is highly disturbed by this.
In the Star Trek: The Next Generation episode "The Chase", Picard's old archeology professor brings him a Kurlan naiskos as a gift. An ancient relic, the figure opens up to reveal several smaller versions of the figure inside.
Speaking of LOST, Howard L. Zukerman keeps diamonds a nested doll in the episode "Exposť".
The TV version of Tinker, Tailor, Soldier, Spy has a traditional Russian one in its intro. Each doll is revealed to have an irate expression until the final one, which is blank. This is reflecting the search for a Russian mole at the heart of MI6.
In one episode of the classic Doctor Who, the Master disguises his TARDIS as a police box, and the Doctor materializes his TARDIS around it. Somehow this results in a large number of TARDISes-within-TARDISes, with the "innermost" one opening to a hitherto-nonexistant back door on the original TARDIS.
In one episode of Castle, Castle and Beckett have to check Eastern European shops to try to find a candy bar the victim had (so that they can hopefully identify her). Beckett tells the captain Castle "had to buy something in every shop!" He's then seen showing off a set of new nesting dolls, gleefully explaining that they defy the laws of physics because "Just when you think there can't be another one..."
The Grangalan outside Costa del Sol can spawn smaller versions of itself known Grangalan Jr. for the second generation and Grangalan Jr. Jr. for the third and smallest generation.
The Black Materia is contained within the Temple of the Ancients. When the party goes in and discovers it, they discover it is actually a replica of the real thing, and the real Black Materia is actually the Temple itself that contains it.
Tweedle Dee and Tweedle Dum from American McGee's Alice can open up and spawn smaller, weaker copies of themselves.
Some treasure chests in Donkey Kong Country games are like this, and the inner chests are inexplicably the exact same size as their containers.
In Devil Survivor 2, the manifested Dragon Stream is one of these. It's a segmented "dragon" made up of heads linked by Nested Mouths. When you beat Mizar, it ends up swallowing Mizar along with every head in the chain until the last is left.
One of the enemies in Alien Hominid is a bunch of robotic Russian Doll bears that fight you partway through the boss.
In Paper Mario: Sticker Star, the boss of World 4 is a gigantic ice statue of Bowser. Once you deplete its health enough, it breaks apart, only to reveal an identical, smaller statue within. This continues until you uncover the one controlling it, a Mr. Blizzard.
The Mammoshka boss in Mario & Luigi: Dream Team. It's a mammoth like creature inside a whole horde of mammoth like shells each slightly bigger than the one inside it. The actual creature even turns out to be less than half the size of the thing you start out by facing!
Ultima makes this a signature of the Guardian's magic constructs, with nearly all of them being hollow geometric objects containing a smaller copy of themselves inside.
One episode of Blues Clues has Steve opening a present with an increasingly smaller present inside each one.
The Living Doll from The Tick has this superpower, hence the page quote.
One Tom and Jerry short, "Safety Second", has Tom cornered by a large firecracker. Instead of blowing up, it breaks apart to reveal a smaller firecracker, which then reveals a smaller firecracker, and so on until all that is left is a tiny firecracker. Tom holds it in his hand and places it on his nose, and then it blows up in a huge explosion.
A couch gag in Season 9 of The Simpsons has Homer run in front of the TV alone and the top half of his body pops off to reveal Marge. Inside Marge is Bart, inside him is Lisa and inside her is Maggie.
In Ultimate Spider-Man, there's a Doombot that contains a smaller Doombot which contains a smaller Doombot and so forth - all of them nasty, right down to the mouse-sized one. They get loose on the SHIELD helicarrier.
There was a Mr Bogus claymation short where Bogus finds a large fruit on the kitchen counter, but each time he cuts it open, the peeling falls apart to reveal a smaller fruit inside, and so on, until he is forced to settle with eating the tiny fruit found in the center.
Why, the matryoshka dolls themselves! A common variation of them is a matryoshka with faces of various Russian leaders, usually from Lenin to Putin.
By definition, baby mammals are smaller versions of their parents.
Marsupials bring up the analogy to perfection.
Aphids take this Up to Eleven. The females are actually born pregnant.
Nested functions are common in computer programming.
A common prank/trick at Christmas is to wrap a special item within multiple layers of boxes.
This is also the basis of the game "Pass the Parcel" - a prize is hidden within multiple layers of packaging and is passed around while music plays. When the music stops whoever's holding the parcel gets to remove one layer.
The smallest scale of model railroad, Z scale (1:220), can be used on larger model railroads to represent a model railroad. Yes, a model railroad featuring a model railroad. XKCDhad fun with this idea.