Y: The Last Man has two issues that focus on a theatre group trying to make important work about the post-Gendercide world. Their first effort is not received well. Later they try films and comics. Also, a supermodel whose profession is obsolete and is now clearing bodies (a minor character from early in the story) gets a issue later on.
Peter David, fed up with the Wolverine Publicity that drives the X-Men franchise, once wrote an issue in his X-Factor featuring none of the usual cast, instead focusing on popular characters like Wolverine and Cable.
In a similar vein, Walt Simonson wrote a three-issue Fantastic Four arc (with art by Arthur Adams) in which the FF are temporarily replaced by the four most over-exposed (during the 90s) characters in the MU: Wolverine, Hulk (during his gray-skinned Mr. Fixit phase), Spider-Man and Ghost Rider.
The classic Uncanny X-Men story Kitty's Fairy Tale. The cover even featured Kitty Pryde announcing, "And now for something completely different!"
Also, issue 6 of The Mighty Thor volume 3. This volume is usually about the female Thor, but instead this issue is a story told by Loki about battles he and the Odinson fought in the 9th century AD. Jane doesn't appear at all, because she's incapacitated thanks to Avengers Standoff. This issue is also in a completely different art style.
The shift from the Brian Michael Bendis Era Avengers to the Jonathan Hickman Era is a very noticeable example. From the more accessible, Bendis-voice-filled Avengers to the more high-concept, sci-fi Hickman Avengers.
After Hickman's Avengers ended the tone changed during All-New, All-Different Avengers with a focus on teenage superheroes and a slightly lighter and softer tone more akin to the Bendis run of Avengers.
After Joss Whedon took over Runaways, he veered sharply away from the usual storyline of the Runaways dealing with some Monster of the Week by sending them back in time to 1907, where Victor falls in love with a local girl, Chase and Nico discover that an earlier version of the Pride is trying to start a gang war, and Karolina and Molly try to rescue a young girl stuck in an abusive marriage to a much older man.
Jon Sable, Freelance #33 is about the children's books that Jon writes and tells the story of a group of leprechauns living in Central Park. Aside from a framing sequence, the art is by Sergio Aragaones instead of Mike Grell.
The Fantastic Four Roast (February, 1982) was a one-shot all-humor special where everyone in the Marvel Universe showed up at a fete for some good-natured riffing on the titular team. Written and laid out by Fred Hembeck, it took the liberty of changing why Dr. Doom became a villain and harbored such hatred for Reed Richards—in college, he wasn't invited to a panty raid with Reed and his college buddies.