Princess Mononoke has two MacGuffins. One is the curse on the main character's arm (a Clingy MacGuffin) which he is trying to remove before he dies from the infection, and the other is the Forest Spirit's head, said to grant eternal life to those who own it. Despite both playing prominent roles neither has any functional impact until their relative plots are resolved at the end.
The Imperial Seal and the Dragon Jade from Ikki Tousen.
Every single episode of Get Backers revolves around one of these. Somewhat justified, as the characters retrieve, transport, protect, etc. things for a living.
In D.Gray-Man both sides of the holy war are actively looking for the heart of Innocence. Nobody knows what it looks like and at this point it hasn't been found yet. Also counts as a Living MacGuffin now that it has been revealed that it has awakened and thus has a wielder.
In One Piece, the titular treasure is a MacGuffin; nobody knows exactly what it is (or even if it's real), but everyone wants to get their hands on it. This is even more evident in the earlier drafts for the manga called "Romance Dawn", where there was no mention of One Piece, and Luffy was a pirate just for the hell of it.
Later chapters hint that some living (and recently living) characters know what it is and that when it is discovered it could possibly alter the entire world, though at this point it still qualifies as a MacGuffin.
The Crystal Flowers from Petite Princess Yucie, giving the Platinum Princess candidates an excuse to visit each other's worlds.
In Piano, Miu's self-composed piano piece is the MacGuffin. Theoretically, the entire series is built around it. In actuality, it takes a back seat to the "slice of life" drama that makes up the story. The audience only really gets to hear it in the first episode, and it's just an extract. The series finishes just as Miu walks on stage to perform it, a source of snarling frustration if the viewer's been wondering just what she's been working on all this time. Still, at least no-one tried to kill her to get their hands on it.
Tthe entire Orange League episodes are caused by Ash trying to get the mysterious GS Ball to a Pokeball expert named Kurt. No one knows what's in it. By the end of the Johto League episodes, it's just forgotten. In the games, the GS Ball was used to make Celebi appear in the Illex Forest. However, Celebi has appeared in the anime/movies since then, with no known connection to the GS Ball. They tried throwing it, using a crowbar, electric saws, and a laser. Nothing worked, and it was completely forgotten about later. Chances are, not even the producers really knew what was in it.
The GS Ball in the anime was supposed to be similar to its role in the games, it was supposed to contain Celebim but the producers decided to use Celebi for the movies, so when they had Ash give the ball to Kurt, the producers left that subplot unsolved in hopes that the audience would forget about it. They didn't.
Also badges and ribbons to some extent.
Definitely, the Key of the Twilight in .hack//SIGN. A common explanation is that it is/offers a power that transcends or contradicts the rules of The World. Everyone chases after it for the entire series, yet no one has the slightest idea what it's supposed to be, often questioning its existence, what it's supposed to do, and why they're even chasing it in the first place. Viewers are still confused about what it's supposed to be but it's commonly accepted to be Aura.
Lupin III has operated as a crook and spy. Nearly every thing you can think of has been a MacGuffin chased by Lupin. Even toilet paper.
From Lupin III (Red Jacket), we have episodes where Goemon and Lupin are competing to get an ancient document from police headquarters, which turns out to be the laws and regulations guide of Japanese policemen... circa 1885 or so, and another such episode where Goemon is up against his former rival-what-killed-his-master, searching for a secret scroll with the final technique. Turns out the scroll is blank, and another one of those Be Yourself metaphor things. The series played with the trope at one point — Lupin is captured by a Rich Idiot with No Day Job and strapped with a bomb; the guy takes Fujiko hostage as well and sends Lupin to steal a file from the police. The file is the rap sheet for a minor criminal, and none of the heroes can work out why he'd want that. Turns out the rich guy is the criminal, with serious plastic surgery.
Barring a scant handful, every... single... movie revolves around a MacGuffin, which is inevitably lost by the end.
In Windy Tales, the wind manipulation powers are used mostly as a backdrop for the more Slice of Life nature of the tales in the title.
The collection of "hanamaru" in Magical Play is mainly used to give the three main characters a reason to hang out with each other.
The flashy, expensive sneakers are the primary (and possibly only) motivators for Kirenenko in Usavich.
Air Gear has the Sky Regalia. It has the ability to control anything that incorporates A-T technology. Because A-Ts really are just small and extremely efficient motors, the technology has been incorporated into almost everything to make it cheaper and more effective. A-T tech has given rise to, among other things, truly massive guns mounted on equally massive platforms, and the Keeper of the Sky Regalia would have control over all of that.
The anime version of Sands of Destruction is about the World Destruction Committee, who spend the entire series carrying around an orb capable of destroying the world. (Only one of them is capable of using it, however, and he has no desire to destroy the world.)
One of Osamu Tezuka's numerous completely fabricated diseases in Black Jack is a disease called 'MacGuffin Syndrome', said to be incurable (or, at least, impossible to heal without a lot of stamina). It was first mentioned as the disease that a character suffers from... take a wild guess at what it's used for.
The demon tool Brew in Soul Eater. Originally sought out by Shibusen for no clear purpose other than to avoid the other guys getting their hands on it, it was used as a bargaining chip by Medusa. She tricked Arachne into thinking she had the real thing, and gave Brew itself to Shinigami in exchange for information and a deal to bring down Arachnaphobia. The one occasion the MacGuffin tool itself does something significant, is in a Chekov's Gun-like moment during the Baba Yaga arc. Its soul amplification ability saves Death the Kid's life. And his left arm. Now placed in Noah's book, it may well turn up again to...be passed around by the cast once more.
Unsurprisingly, it does. At the very end of the series Crona uses it to seal Asura, and hirself, on the moon.
In a sidestory in the Fruits Basket manga, Akito's mother, Ren, and Akito manipulate various people in their family over the possession of a box left behind by Akito's father, Akira. When the box is opened, it's empty. Akito's caretakers said Akira's soul was in the box, but Akito had long since stopped believing that and just used the mystery surrounding the box to jerk Ren around.
The Shinzaho in Fushigi Yuugi (Takiko's necklace which originally belonged to Anlu the Oracle, Suzuno's hand mirror that she brought from the Real World, Yui's earring that she wore in the summoning of Seiryuu, and Miaka's ring and later her and Taka's unborn child). Used to summon The Four Gods, especially if (for some reason) the summoning ceremony can't be performed normally. Half the plot is therefore the search for them.
The Dokuro Stones from Yatterman would definitely apply.
The Eto Gun from Et Cetera. Very nearly EVERYONE Ming Chao meets is after it.
Celty's head in Durarara!! is a MacGuffin that falls in and out of focus, as no one who has it knows quite what to do with it, and Celty herself isn't sure she wants it.
In the original Sailor Moon anime series, there were what the dub called "Rainbow Jewels", seven gems that would bring about the Silver Crystal. The Dark Kingdom wanted it to gain the power they needed to unleash Queen Metallia, Tuxedo Mask wanted it to help with his memories and the Sailors just wanted to keep them safe. The bad guys get them for all of five seconds before they become the Silver Crystal and end up revealing that Sailor Moon's also the missing Moon Princess.
From Eroica with Love is at least partly a spy story, so naturally it's chock full of these. Mostly microfim, but also various objets d'art.