Simply put: If it's popular and has an associated message board, you're bound to stumble upon fan wars at one point or another.
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Achewood, which began as a very patchy set of one-shots elevated by the Lie Bot, what is the saddest thing strips, and developed into a subtle, clever strip with several deep interesting characters ORAchewood, which began as a daring and hilarious absurdest web comic, and got "ruined FOREVER!" when Onstad sold out and started having continuing storylines and jokes that made sense.
Conversely, many feel follow the first interpretation but believe that the strip has become so surreal, stylistic and referential that it's begun to lost its grip on those deep, interesting characters.
Collar 6: Should the world be complete fantasy, or should the characters analyze how dysfunctional their relationships are.
Ironically, the LiveJournal fans, which are far kinder, appear to average between three and four new topics a month, while the Keen Spot forum (the most vocal hatedom) has an active community and posts a thread for every new comic strip. It was debated whether Mookie was hanging a lampshade on his fans with Gregory Deegan's line at the end of this strip.
For context, prior to the 07 October revision, page 83 featured Charlie performing a sexual act on Jamie against his explicit consent, and Jamie dis-associating so as to make the experience pass more quickly. Although the arguments surrounding Charlie's actions against Jamie had many, MANY intricate and painful facets, the biggest and/or loudest camps were divided primarily between A: Those who felt that Tab's choice to make Charlie commit an act of sexual violence played dangerously into a larger trans-phobic cultural narrative, and B: those who either saw Charlie's actions as —if not forgivable— comprehensible given her extensive back story, or who focused on other things like the fact that it honestly portrayed a man as being susceptible to sexual abuse, in spite of a number cultural assumptions to the contrary. There was a LOT more to it than just that, but better to be brief and LetOtherArticlesWithBetterWriters give you an idea of some of the complexities involved. The original massive and contentious comment thread has since been taken down, though Tab has said that he is keeping a copy for posterity.
Looking for Group when it was finally confirmed that Cale and Benny are romantically involved, some fans responded with great wailing and gnashing of teeth and promises to never read the comic again, while others were jumping for joy.
There's the base of Megatokyo arguments, of Old Story (with Caston) Vs. New Story (Fred by himself), which then fractions into the characters themselves, all (literally, even minor, minor, minor characters) of whom no one can decide as to how they're portrayed.
Homestuck's fanbase argues about everything. And we do mean everything, listing all the points of contention would take up most of this page. It's gotten to the point where a former mod had himself permabanned from the forums.
Of particular note is the debate over Vriska, which if anything has gotten more heated since her death.
SinFest started its path towards the broken base around 10/2011 with the arrival of Xanthe Justice and her Sisterhood arc. Is now pretty much a civil war.
The presence of storylines in Video Review Shows. Some see them as a great way to see what else the reviewer is capable of, some find them generally entertaining, or don't see a problem with them. Others find that it makes it hard to take the review seriously, find them lacking, and point out how it can take time away from the actual substance they came to see. Some even would be fine with them if not for their prevalence and for the Follow the Leader tendencies from That Guy Withthe Glasses.
The Spoony One's departure from TGWTG practically shattered the base. Did Spoony quit or get himself fired? Did he reveal himself to be a sexist, petulant asshole who couldn't get that he crossed the line with his joke to JesuOtaku, or was he the victim of the collaboration of Obscurus Lupa and Lord Kat, who got involved with something that was none of their business? The fact that Spoony later admitted to his own psychological issues and finally getting the proper treatment for them may have quelled the online war between the Broken Base - somewhat.
The Mondo Media Youtube Channel deals with a lot of this. On one side of the subscribers, who have the people only subscribing for Happy Tree Friends and Dick Figures, and anytime Mondo uploads a new series or episode of that new series, they will comment asking for more Happy Tree Friends or Dick Figures, while the other side apperciates the newer shows and will tell the other fandom to shut up.
The character approval process used in the Global Guardians PBEM Universe created this effect among the players. Specifically, every proposed character was examined with a fine tooth comb, the maths were run and rerun, and everything was compared to the character's central concept and the standards of the setting as a whole. Unacceptable characters were rejected, or heavily modified. Some players found this refreshing and liked the process, while others found it infuriating and hated it. There was no middle ground.
On a similar token, Survival of the Fittest v5 has become somewhat more stringent and much less personal with its character evaluation process than previous versions. A fair few veterans have left because they don't like the change of atmosphere.
Go into any well-frequented NationStates IRC room or forum and ask what the real point of the game is. Then stand way back. The NS page says there are two ways to play it, but it's more like seven. Fortunately for the fanbase, each group mostly keeps to themselves and tries to keep the others at arm's length.
BikdipOnABus's fans either love or hate his new girlfriend being in his videos.
The Slender Man Mythos, due to the Running the Asylum nature of the mythos, is almost this by definition. Since Victor Surge, the man who posted the first images of the Slender Man, has stepped back to let fans run things, no one but Surge can claim to be the original creator and there's an unwritten "everything is canon" rule. Fans are divided on almost every aspect. Some consider Marble Hornets, Tribe Twelve, and Everyman HYBRID the only series worth watching, many say that only one of the three is good, and some fans consider "Surgism" the only way to go. Fans will debate over whether or not Marble Hornets (the most well-known series) has "sold out," there are very different opinions of crossovers of any sort, and of course, there's the eternal vlog vs. blog debate....
That's not even counting the in-fighting between various forums, facebook groups, and even drama that's not related to the story in specific AR Gs and series fanbases...
Slenderman himself has become one due to how ingrained in Creepypasta he's become and how much the original content is related to, or inspired by him. The Creepypasta wiki even banned the posting of any more content that even looked Slenderman related.
Neurotically Yours. The Reset Button, Art Shift, and combination of the secondary series's into Neurotically Yours. Some find it a fresh breath of air to the series, and a good idea. Others can't stand the new art style, and reset story, and have quit watching it altogether.
Game Grumps, despite being a relatively new LP series, already has a three-way battle amongst is fandom regarding their New Super Mario Bros. Wii playthrough. On the one hand, you've got fans who wish they would stop comparing it to older games and just enjoy it for what it is. On the other hand, you've got fans who say that Egoraptor and Jon Tron are entitled their opinion and that they can criticize the games if they want. On the third hand, you've got fans who wish they'd just start making jokes while playing again.
Jon Tron was a huge base breaker among members of the fandom. There were those who thought he was genuinely funny and entertaining, those who felt he was annoying and took away from Arin's entertainment value, and those who felt that he was funny on his own show but terrible in Game Grumps.
And then Jon left and was replaced by Danny from Ninja Sex Party. Is he a good replacement for Jon or not? It doesn't help that people who complained about Jon being on the show then suddenly started complaining about him leaving. The controversy has died down a bit, however.
Steam Train. It doesn't help that it began around the same time that Danny became the new "Not-So-Grump". Some fans love it, some hate it, and some feel that it's good but should be its own separate channel.
Any time the Grumps have difficulty figuring out various aspects of a game. Fans are divided over whether or not they should just be having fun and enjoying the game at their own pace, or that they should learn to play the game "correctly" instead of wasting everyone's time. The Grumps themselves tend to lampshade this by joking about how they struggled during moments that were obvious in hindsight.