Every alien race in Buck Godot: Zap Gun for Hire gets into a holy war at the same time to get "The Winslow", a furry alligator-like creature that has extreme religious significance. The Winslow's purpose is to be a Shaped Like Itself MacGuffin. A secondary purpose and/or effect of its primary purpose is to confuse everyone.
Lampshade Hanging in the Tenchi Muyo! comic by Pioneer, in which Sasami has a special delivered package from Jyurai, which turns out to be MacGuffins, light and tasty delicacies that resemble muffins. In fact, they're so good "why else would people chase after them?"
The Secret Six ongoing kicked off with an arc centering around a rather interesting MacGuffin: a get out of Hell free card.
In one issue, Jon is hired to retrieve a stolen formula (codenamed 7X) in a sealed envelope, with strict instructions that the envelope is not to be opened. Jon succeeds and returns the formula to its owners. Although he didn't open the envelope, he comments that when it got wet the envelope went transparent and he could read the list of ingredients and there isn't anything there that cannot be bought at a corner drug store. The executives comment that the point is that no one else knows that and burn the envelope. 7X turns out to be the formula for Coca-Cola.
Another story revolves around one of fiction's most famous MacGuffins, the Maltese Falcon — specifically, the prop Maltese Falcon used in the 1941 film, now an extremely valuable collectible.
Tintin: The Arumbayan statue in The Broken Ear (the Real Life artifact Hergé based it on belongs to the Royal Museums of Art and History in Brussels).
The albatross in Cerebus the Aardvark, which was vital to establish who would be the proper pope over the Eastern and Western Churches of Tarim in the High Society and Church and State arcs.
The Exploding Nanites in the Thunderbolts' blood that keep the Boxed Crooks contained are referred to as a MacGuffin by Bullseye in #125.
The lump of bombastium in Carl Barks's "A Cold Bargain": an Idiot Ball and MacGuffin rolled into one, made of pure Unobtainium. No-one knows what it does, but since it's so rare that the substance isn't found anywhere else outside that one lump, and because they don't actually know it doesn't do something amazing, everyone wants it. Scrooge McDuck bids an enormous sum on it on impulse and then has to go to great lengths to maintain the possibly useless lump's existence. In the end, it turns out it can be used to make loads and loads of ice cream, which does make the deal profitable.
And of course there are all the other Scrooge stories with MacGuffins: the crown in "Lost Crown of Genghis Khan", the locket in "Lemming With the Locket", etc.
In the second issue of the comic book adaptation of Sonic X, Sonic and friends investigate a sunken ship owned by the long-dead pirate "Captain Seamus "Red-Eye" MacGuffin", and later outright call the ship "The MacGuffin". Subtle, it is not.