The "Haley speaks in cryptograms" story arc of The Order of the Stick was largely regarded as a Dork Age while it was transpiring, given that it took the only female protagonistnote well, maybe. We're still not sure about Vaarsuvius and eliminated her ability to deliver the verbal humor for which the strip is known for over 100 strips. The climax of the plot may have made up for it in the minds of some fans, however, as it ushered in the Haley-Elan relationship and gave crucial character development to both characters. Still, the actual aphasia has only rarely been mentioned since it disappeared.
Sonic the Comic – Online! seemed to go through one for ages after the syndicate arc. The series' main villain, Dr. Robotnik, had disappeared, his second-in-command Grimer had gone quiet, and Sonic was constantly dealing with the actions of an insect mafia called "The Family" and a media slur campaign. This went on for a good ten issues (at a time when the comic was releasing three to four issues a year), and suffered from a lot of Schedule Slip and filler. This all built up to issue 249 when Grimer was said to be behind everything, only for three successive specials to come out to try and finish off all the pre-250 stuff planned so that 250 would make sense (see the aforementioned Schedule Slip). 250 then revealed the return of Robotnik as a supercomputer controlling a lot of Mobius.
This went exactly nowhere as, despite this sudden and massive change in Status Quo, with the whole planet at war against Robotnik's machines, it took another four issues for Robotnik to actually reappear, during which time pretty much every character's story refused to acknowledge the main status quo, with one character dealing with magical beings from another dimension, another dealing with an adventure in a magical dimension, a third story about two characters who were stuck on another planet, and the fourth story slot taken up by a four part House of the Dead story that many people grew sick of due to bad Purple Prose-filled dialogue.
The creator of Collar 6 himself has expressed this opinion about the comic's second arc. Not only was it long, starting in March 2011 and ending in January 2014, it drifted away from the usual BDSM comedy in favor of a gritty action plot. And the move from 3 pages a week to 5 pages a week brought a dip in art quality as well. Fans and creator alike were relieved to see it finally over and done with.
Many readers feel this way about Sinfest artist/writer Tatsuya Ishida's sudden "conversion" to feminism eleven years into the comic's run, coinciding with the return of future Creator's Pet Xanthe/"Tricycle Girl". From there, the comic steadily lost much of its good-natured humor and steadily gained Strawman Political rants about the suffering women face under the oppression of the "patriarchy".
Megatokyo has been in one for years now; even Word of God acknowledges it. The comic shifted around the late 2000s and early 2010s from a charming exploration of American weeaboo culture to a pretentious love story pairing humans and robots.
Saturday Morning Breakfast Cereal is often seen as having gotten more political and righteous about the power of science while the strips numbered in the 100s or 200s.
Ctrl+Alt+Del was divisive to begin with, but ran into an arguably ongoing Dork Age hard starting with the infamous "Loss" strip and Lilah's miscarriage. Ever since, writer Tim Buckley has continually tried to juggle the wacky video game related antics from the series' infancy with dark, depressing drama, to little success. Much fun has been made of the inclusion of such themes as robots modded from Xboxes (which had only ever been Played for Laughs prior) initiating a Bad Future - an arc which, let it be mentioned, ended with The Hero Dies and a Continuity Reboot - in a comic that has always advertised itself as goofy gaming comedy.
Homestuck had a bit of this during the early parts of act 6, with the entire central cast replaced with new characters, and the showy fate-of-the-universe plot being sidelined in favor of act 1-style messing around and a Romantic Plot Tumor. however, as it was implied from the get go that this would be temporary, it's not a perfectly straight example.
In some ways, the comic started in one. The first 1500 or so pages are often mocked even by the fans for setting up concepts so absurdly complicated that it's a test of faith not to throw the comic away.