The side story the Flower Knight in Drowtales. To win the heart of the queen of their city, a knight ventures out into the world to find the most beautiful flower on earth. He fights his way through countless hardships for years, until he finally finds the flower he was looking for. He brings it back to the queen, wins her heart and the two go on to produce countless children... well, the flower he brought back produced countless seedlings and new flowers, until all in the city owned their own... It is then the flowers reveal their true nature, a deadly parasite that sucks the life out of everyone in the city, killing every single person in it, leaving the Flower Knight the only survivor among a grave of his family and subjects. He leaves to the surface, to find and destroy the being that gave him the flower and destroyed all he held dear with it. The story ends there and rather he succeeded he or not is unknown. The flower has since made a reappearance, again, controlled by the Big Bad Snadya'rune, who seemingly plans to unleash the same horrific fate once again.
The ending of the seven year long webcomic Bob and George shows that pretty much the whole comic was a plot by the title characters' mother to make George willing to kill Bob (his super villain brother) if necessary and for Bob to be aware of it. In a subversion or at least avoidance of Shoot the Shaggy Dog, however, a comment during the finale prevented the deaths of just about everyone in the Cataclysm.
In GastroPhobia, almost all the chapters end with the plot getting humorously undermined.
Not quite. There are indeed a number of Shaggy Dog Stories in 8-Bit Theater, such as the Chocobo Breeding arc and the random town arc from right before the Orb of Air quest, but most of the story arcs don't fit the definition. They tend to end in anticlimaxes, but the anticlimaxes themselves do further the plot.
Turns out the entire plot is one of these; while the Light Warriors are arguing with each other yet again, the Big Bad is killed by a minor character using a strategy Black Mage had scoffed at in one of the series' first comics. After nine years and 1200 comics, the main characters end up basically where they started off without really accomplishing anything outside of causing problems wherever they went. According to the author, this was his plan from the very beginning.
The first season of Ansem Retort ended like this. After a demon invasion, fighting through FOX headquarters, one character fighting Ansem, another getting god-like powers, and using said powers to summon a dragon with a nuke on its back, the president of FOX was defeated by a stab in the back. Of course, this is lampshaded:
Marluxia: That's it? Axel stabs the guy and we all go home?
Zexion: Screw you. They're dead, we're alive. We win, they lose, end of story. Who's up for Chinese food?
One story arc in Blip. K is speaking with Bang over the cell phone, and she hears as he gets attacked by someone with a knife. Fearing the worst, K enlists a friend and drives from San Francisco to Los Angeles to make sure Bang doesn't bleed to death in a parking garage. They can't find him at the parking garage, nor at any hospitals. When they finally check Bang's apartment, they discover that he's completely okay, and they needn't have worried about him at all.
Susan's uniform crusade was cut short when The principal revoked the dress code after parents complained about having to wash them daily.
The race through Swedekia in the Temple of Swedish Furniture arc also qualifies. The last TV stand that Elliot and Noah were racing for had already been purchased the previous day, and the store's online inventory didn't register that piece of information.
Some PvP's storylines in the last couple of years have been massive buildups leading to either tremendous jokes or epic storylines, only to fizzle out on a short, mediocre anticlimax.
Much of the humor in pictures for sad children revolves around awkward, drawn out, just uncomfortable (and usually surreal) conversation with no conventional punchline at the end.
Irregular Webcomic!: In the Fantasy arc, in strip 516, the heroes receive their epic quest to find the Ruby of Dwarven Might. About 2500 strips later, they finally locate the Ruby: one of them had been wearing it around his neck since the beginning of the quest, completely unaware of its true origin.
The Electric Wonderland comic "Day of Fools" has Trawn race to warn Aerynn of a scan for hackers and magicians. She fails to warn Aerynn in time, but it turns out the scans never detect Aerynn's brand of magic.
Brawl in the Family has comic number 260. This has Princess Peach actually do something instead of just sitting around in a game but, upon escaping the castle, she notices Mario going in, and secretly follows him up until after he defeats Bowser, when the two finally meet. Mario, who doesn't know she's managed by herself, explains that he's here to save her. Peach simply shrugs and says "My hero."
Frequently used in Mountain Time, but most notable in one instance that took 12 episodes to reach its shaggy conclusion — notable because Mountain Time stories hardly ever last more than one episode.
DM of the Rings, a webcomic running the plot of The Lord of the Rings, is resolved in exactly the same way as the book... Except Frodo and Sam aren't Player Characters at that point. Aragorn, Gimli and Legolas are, and are essentially railroaded into distracting the Big Bad and doing nothing of value while an NPC wins the campaign by succeeding at a Will Save. The players are underwhelmed.
This strip of Something of that Ilk even references the trope in its title.
Arguably FreakAngels could fit in here. After years of buildup as to their nature and purpose, the Freakangels eventually ascended into a Steampunk future since the world wasn't ready for them...and that was that. No answers and no explanations.
L's Empire spend over 400 pages gathering the shards of the Master Stars. It turns out that only the last one was important to Dark Star's plans and the other 25 were entirely superfluous. Void lampshades this when they find out.
Ozy and Millie: Felicia starts dyeing her wool black, which scares the school staff into prohibiting black wool. Millie, despite hating Felicia, gets indignant at this suppression of the right to freedom of expression, and covers herself with black cotton balls in protest, only to find that Felicia surrendered to the dress code without a fight and sheared herself.