Gunnerkrigg Court: Chapter 10 - "Dr. Disaster Versus the Creepy Space Aliens from Outer Space". The main Urban Fantasy plot took a break for a comedic Raygun Gothic interlude—though not without some character development.
There are also some unusual interludes following the end of each print volume. The first was followed by Guest Strips and letters between the characters; the second was followed by City Face, a short and bizarre story about talking pigeons, which was so popular it got a sequel in the next volume. Though not part of the comic proper, Tom has said that most of these materials are canon. Somehow.
There's also the "Annie watches Kat play GTA" comic, the "Kat melodramatically plays MGS" episode, and the similar one where they all watch Princess Mononoke.
The delightfully campy Fans! has featured, among other things: A musical arc (with pictures of characters singing and links to the sound files underneath), a story told from the perspective of an FIB agent experimenting with mind control techniques told via his blog, and a story done entirely in chat logs.
Sluggy Freelance did its fifth-year anniversary in flash animation (no, no voices, just animation).
Most stories in The Wotch, put the focus on the title character and here two friends, usually including a B story that either focuses on one of the main characters, or, less frequently, a minor side character (like "Moon Over Tandy"). However, "A Girl and her Blob" took a different approach. There is a side story about Anne and her friends battling Were-creatures and a Mad Wizard, but the central story is on minor character Ming and Myrrh, a blob-like woman Ming discovers and bonds with.
The Intermission between the third and fourth acts of Homestuck drops the main storyline completely and shows a storyline involving alternate universe counterparts of some of our characters, who have (in this new story) formed a gang called the Midnight Crew. Their ...behavior becomes a plot point later on.
The Fan has the Sheyleron Saga side story, that is not only completely unrelated the main storyline, it takes place in a completely different universe, yet the author insists on sticking an installment to the end of every single episode, and sometimes, right in the middle of one.
An intermission comic in The Order of the Stick was done as a parody of the old "Let's Go Out to the Lobby" advertisements seen at movie theaters. One group of concession stand snacks is challenged by another, and an epic D&D style battle ensues.
After three lengthy story-arcs, Nature of Nature's Art went on to... a gag-a-day-style strip called Wild Style. It's an "intermission arc", so to speak.