Broken Base/Web Comics

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.

Webcomics

 * 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 OR Achewood, 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.
 * Dominic Deegan. Whether it's the death and perceived vilification of Siegfried, the Super Greg arc, accusations of Mary Sue, The Chosen One, Jumping the Shark, and Unfortunate Implications being flung about, the Unpleasable Fanbase nitpicking everything out of spite (or because it's fun), or the forums dissolving into Deadpan Snarkers, Hatedom, and cries of Ruined FOREVER and They Changed It, Now It Sucks, it's a wonder the fandom hasn't imploded by now. Since there are indeed still fans who love the comic as much as ever, are willing to forgive Mookie his mistakes, or who simply don't see them as mistakes because of their Willing Suspension of Disbelief. They're simply less vocal, it seems. Perhaps they fear FanHaters.
 * Ironically, the LiveJournal fans, which are far kinder, appear to average between three and four new topics a month, while the Keenspot 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.
 * 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.
 * Order of the Stick, over whether or not the series has become better or worse since it became subjected to Cerebus Syndrome.
 * Also whether or not Vaarsuvius'  and Haley's  were justifiable I Did What I Had to Do moments or indefensible crossings of the Moral Event Horizon.
 * Miko fans vs. Miko haters.
 * 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,

Web Original

 * 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.
 * 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 (or unfortunately) 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....
 * 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.