Badass Decay: Haseo, after being Data Drained by Azure Flame Kite.
Broken Base: The best way to create conflict in the .hack fandom? Ask which one is better: The World R:1 or The World R:2. Watch it burn.
Arguably everything after R:2. While individual fan opinion varies per product, everyone agrees that the quality became schizophrenic and dragged the series down as a result. It's also not helped by the fact that basically everything short of a couple OVAs remained Japan-only.
The reveals in Beyond the World and the supplemental Thanatos Report with Versus, mainly the fact that the founders of ALTIMIT and the woman Harald pined for known as Emma Wielant were all part of an Eco-Terrorist group as one grand conspiracy that retroactively caused the entire plot of the whole franchise for their own goals. Because of the nature of these materials, most fans don't even know about these twists, and considering the absolute hell that resulted among the fans that do, that's probably for the better.
Fanon Discontinuity: The Broken Base example above about the massive twist that changed a lot of backstory context for the series united some of the remains of the western fanbase in proclaiming that it simply didn't happen. The fact that there's not many people outside of Japan that even know about the twist to begin with doesn't help.
Genius Bonus: The Knight Templar in Twilight Bracelet, who declares herself equal to a god of The World, is named Kamui- the Ainu word for "god".
Hilarious in Hindsight: Let's see, a familiar face shows up again, albeit looking incredibly creepy, almost zombie-like. It doesn't talk, stalks the players and the world they are in, never uttering a single word, just fighting you, or nagging you. Who are we talking about? Herobrine or Azure Flame Kite?
Haseo and Endrance, of .hack//G.U.. Aside from Haseo being able to marry Endrance along with most of the girls in the Marriage Event at the end of Volume 3, telling Silabus and Yata "I need you." during the male-dominated Friendship Events was interesting. There's also an e-mail conversation the player can have with Kuhn which includes the option of Haseo telling him that he's in love with him. Kuhn laughs it off as a joke and Haseo's follow up is nothing special but still...
There's also the sequence at the end of the 100 floor (no shit) bonus dungeon. After you beat a tough boss, you get a scene with Ovan. He sounds like he's half in love with Haseo.
Vol 4, made specfically for the HD remaster, finally lets Ovan join the party and gives him two endings; one is a standard freindship ending, the other is a marriage ending. Which one you get depends on a single dialogue choice, though it's implied Ovan misinterprets Haseo's words (either accidentally or on purpose) in the latter, along with Haseo doing the same (Definitely on accident), and it's semi-played for laughs with Haseo being the one to wear the dress, protesting the entire time to the whole thing, and doubly protesting to the dress.
Female example: Due to If It's You, It's Okay (or maybe Bi the Way?). Subaru becomes romantically attached to Tsukasa, and the fact that "he" is a girl in real life doesn't deter Subaru in the slightest. It's suggested that after college, they began living together.
It's the Same, Now It Sucks!: The R1 games got quite a bit of flak for having the exact same gameplay mechanics throughout. This problem becomes a lot more understandable if you see the quadrology as one gigantic game split into four (like The Lord of the Rings film trilogy.)
In fact, by analyzing the game data for Infection, it's possible to find almost every single equipment and regular enemy in there (some of them were modified in the later games, however). Actually, it isone game split in four, as there's probably enough room in a single game to hold everything: there's a huge dummy file on each game with the only purpose to raise the game's size to the minimum required for a PS2 game.
Presumably because of this the G.U. trilogy slightly changed up the game mechanics every volume by way of Haseo's job upgrades giving him new weapon choices and new awakenings.
There are a few nasty folks in the story, but none hold a candle to G.U.'s Sakaki, who gleefully exploited Atoli's many emotional weaknesses in order to dominate her, long before AIDA gave him a chance to take over the world from within the network. Even the fact that he himself was the victim of some Magnificent Bastardry at the hands of Ovan doesn't diminish the satisfaction of seeing him cornered and (presumably) data-drained by Aura's knights, as he screams in helpless despair.
CC Corp, a sort of fictionalized take of the developers of the franchise in a Leaning on the Fourth Wall sort of way, repeatedly demonstrate themselves to be some of the worst minds in the whole series. A complete apathy towards the healthiness of their playerbase, notorious business tactics that involve monopolizing the internet and MMO gaming, and are apparently bad enough internally that there's a Token Good Teammate in almost every installment that gets disgusted with them. But that doesn't even scratch the surface, especially with the Lost Ones where they always try to sweep coma victims under the rug so it doesn't cut into profit margins (when they aren't personally responsible for it in the first place). The further into the .hack franchise you get, the more event horizons they liberally cross with a skip and a damned hop.
Player Killing is taken as such a Serious Business affair that G.U. has entire plot lines and characters dedicated to the premise. This wouldn't normally bat an eye, up until people start screaming in genuine terror and throwing out death gurgles from getting their asses kicked in an online game. Not to mention the Moon Tree guild being known in-universe for practically giving every PKer they can find (and Haseo) lectures about how bad they're being and how they ruin the game for people.
So Bad, It's Good: Link has not been well accepted by many; at first due to the Off-Model art style at the opening, the fact that you can only have two player parties (Likely due to the console used), And of course the rampant character assaination of most of the past-series characters part of the game's main story in favor of glorifying it's idiot protagonist, but the story of AIKA has been given praise and the fact that the ACTUAL art style looked good as well. The more people that have played the partially-fan-translated versions however, quickly learn why the game was skipped in it's import.
Viewer Gender Confusion: Tsukasa's actual gender is made clear in the first episode, but The Reveal often evaded those with short attention spans. North American fandom was inundated with Male!Tsukasa fanworks... until later in the series, when The Reveal was stated in script.
Erin Fitzgerald tries to adopt a tough voice for Alkaid, but ends up sounding exactly how female voice actresses sound for young male roles, making Alkaid sound like a boy, which led to people wonder if she was a boy playing a female character.