Every other Uncle Scrooge Comic Story, and to a lesser extent, DuckTales, is essentially a search for a historical MacGuffin. It matters not whether the already-ultra-rich McDuck searches for the Golden Fleece, Solomon's Mines, the remnants of the Trojan Horse, the Crown of the Crusader Kings, the Candy-Striped Ruby etc. so much as it's something valuable for both him and Glomgold to get involved.
Don Rosa's life stories of Scrooge McDuck make this even more explicit by detailing his adventures around in search of wealth, and the sharp downturn after he could just lie back and manage it. The treasures he's now seeking are less important than the ability to zoom halfway across the planet to do it.
An episode of the Sam & Max: Freelance Police cartoon revolved around the heroes chasing an FDA inspector, trying to feed him a sample of their favorite snack food so that he'll realize how delicious they are and lift the ban he's placed on them. The snack food? "Glazed MacGuffins".
Codename: Kids Next Door, "Operation R.E.P.O.R.T." refers to its MacGuffin as The Goods until practically the end of the story, where it turns out to just be a pizza they were suppose to get. But at least they actually reveal it... the mysterious ice cream flavor that Numbuh 5 and the DCFDTL were fighting over in "Operation F.L.A.V.O.R." gets "name-cancelled" the only time it's going to be mentioned, when the others have phoned Numbuh 5.
In an episode of G.I. Joe, Shipwreck finds himself conscripted into entertaining a group of children while the other Joes guard a machine actually called "The MacGuffin Device". Neither the Joes nor Cobra knows what the thing does, they just don't want the other side to have it.
The Taz-Mania episode "Road To Tazmania" is in the same vein, with secret agents chasing two Tasmanian Devils with a certain orange juice box, right down to ending on the opening of the container without revealing what's in it.
The Golden Disk in Transformers: Beast Wars started as a MacGuffin... but in the second season, it evolved out of that status, with Megatron demonstrating exactly what it was and why it was so dangerous in his hands.
The Anti-Life Equation in the DC Animated Universe. Several villains, most notably Darkseid, want it, and the chase for it is a recurring plot point. The equation itself, on the other hand, is not: What it does remains undefined and the two who finally get their hands on it promptly vanish from this reality. (The comic book version, on the other hand, does define the Equation, and some of those seeking it have been able to use it. It's an empirical scientific formula which demonstrates the meaninglessness and futility of existence, which allows one to control the will of others entirely. Its ominous name comes from the idea that "if someone possesses absolute control over you - you're not really alive." Scott "Mr. Miracle" Free has known the Equation all along but chooses not to use it.)
Darkseid isn't the most notable villain to want it; he's the only one who wants it, and the fact that in the finale` another villain Lex Luthor gets a hold of it is rather incidental Lex only has it because he was looking for something, anything, to defeat Darkseid, and thats just what he was given. Darkseid doesn't actually spend much time searching for the Equation either and usually is out to conquer Earth and screw with Superman. The closest he gets to searching for it is one story where he reprogrammes Brainiac and refers to him as "his solution to the Anti-Life Equation", meaning rather than look for the thing he'd decided to actually use a substitute.
In an American Idol parody episode of The Simpsons, the prize winner gets to star in their own "Itchy and Scratchy" episode. After that, it is never brought up again in the episode.
The plot of Kung Fu Panda, to an extent, revolves around the Dragon Scroll—who gets it, who deserves it, how and when it will be used. Tai Lung went to the Dark Side because he was not granted it, then spends twenty years in prison thinking of nothing else, escaping only when he learns it will be given to someone else. The Furious Five, meanwhile, all want it so they can stop the Big Bad and prove their worth to their master, while everyone from Shifu on down to Po believes the panda needs it and its ultimate power to win. The final battle is an endless series of hot potato tosses back and forth around the village square, with Tai Lung and Po constantly in pursuit of each other to get the scroll back.
The kicker? The scroll is blank, without any special secret written on it. The double kicker? What seems a worthless artifact is actually a reflective parchment geared to make Po gain the confidence to believe in the Be Yourself lesson. Tai Lung doesn't get it at all, and thinks it really is a worthless MacGuffin which he has wasted his whole life pursuing. The rage this discovery produces contributes strongly to Po's victory.
At least two episodes of Kim Possible revolve around a pure MacGuffin: in "Sick Day" it's "Ray X" which is repeatedly stolen and recovered when the players are incapacitated by a cold they pass to each other (and "Ray X" is revealed to be a cure for the common cold, after it has been destroyed). "Adventures In Rufus-Sitting" sees the Non-Human Sidekick Rufus swallow a microchip - pursed by three villains and protected by Kim.
Another is the Pan Dimensional Vortex Inducer. Dr. Drakken says outright that he only wants it because his rival Professor Dementor has it. No-one but Dementor and its inventors even know what it does until near the end.
Several episodes of The Secret Show revolve around the U.Z.Z. agents trying to prevent the theft of "The Secret Thing," which is so secret that nobody knows what it is or what it does, but everyone wants it just the same.
The Crystal Coconut in Donkey Kong Country is almost always in danger of being stolen by the Kremlings.
The episode 'Vanessesary Roughness" involves a four-way struggle between Perry the Platypus, Vanessa Doofenshmirtz and Ferb, Baljeet and Buford, and Candace to get a tube of "pizzazium infinionite".
Lampshaded later in the aptly-titled episode "Finding Mary McGuffin", in which Phineas and Ferb track down Candace's lost Mary McGuffin doll. A line near the end makes it clear it's not a coincidence to boot, when a fight between Vanessa and Candace over the titular doll leads Ferb to comment, "This is exactly why they took that doll off the market."
Acknowledged in an episode of Sabrina: The Animated Series when Sabrina and Chloe find themselves trapped inside a video game. The only way to escape is to retrieve an artifact from a citadel at the other end of the country. What's this item called? The Golden MacGuffin.
Lampshaded in the Ultimate Spider-Man episode "Ultimate Deadpool", where the agent Deadpool has to retrieve a list of SHIELD agents from is named "Agent McGuffin." It's also the first clue that Deadpool isn't being entirely on-the-level about what's going on.
Lampshaded in Uncle Grandpa, which had an Indiana Jones parody in which the title character and a young lady embark on an adventure to find a MacGuffin, which turns out to be the most delicious burger at a fast-food restaurant.