Word of God has stated that the "I ban any love or friendly relationships with women so I can focus on the game" he gave Saphir was meant to establish that he's not homosexual. Nothing was said about him being bisexual or in the closet, however.
Sparadrap (and eventually others): Not taking the game seriously enough or taking the right distance from it?
As mentioned in the Ship Tease entry, the relationship between Omega Zell and Gaea, meant to be genuine hate later accompanied by a form of rivalry, gets interpreted as Belligerent Sexual Tension by quite a few fans.
Tabris: The Big Bad or only a Crazy Survivalist to whom the threatening parties happen to be every single living sentient native of Olydri?
Alt Itis: In-Universe. All elements of the Double Play entry from the main page are actually mild cases of it. In one of the books, Arthéon is stated to have another avatar in each of the game's classes because of his background interest (but they're all guildless and stuck somewhere between levels 1 and 10 because of that), making him the only known possible case of the full-blown condition. Saphir also implied that the reroll that she modified to look like Gaea in the webseries was one of several.
Badass Decay: Arthéon, when he was suddenly sent from level 100 to level 1. Dark Avenger also, in parallel to his Villain Decay.
Better on DVD: The Schedule Slip that the webseries experienced a handful of times during its run made it hard to follow for some fans that discovered it while it was still in production and hence watched the episodes as they came out.
Broken Base: As yet another victim of Cerebus Syndrome, Noob is either a funny series that started becoming boring/complicated in Season 3 or a string of short gags that slowly mutated into something with a story.
Canon Fodder: The story left Fantöm believing he has a debt towards every single member of the Noob guild. It has only been repayed to Omega Zell and possibly Arthéon so far. The fourth novel explicitly says that Gaea's is still pending and that she has no intention of letting it go to waste.
Can't Un-Hear It: The live action version is the one that came first, so good luck not reading the novels and comics with the voices of the actors in your head.
Foe Romance Subtext: Fantöm and Spectre, Sparadrap and Dark Avenger to a lesser and one-sided extent.
Girl-Show Ghetto: Some of the shows on Feminine TV are treated as this in-universe.
Growing the Beard: Both the webseries and the comic went through a phase of being rather episodic before having the Myth Arc become visible. The "watch more before giving a bad critic" threshold seems to happen around the Mortegarde double episode (12 and 13 of Season 1).
The first mention of the Roxxor guild in the webseries is a shopkeeper mentioning that their tabards are on sale (i.e. at a cheaper price than normal). It only turns out to be the Coalition number one guild in the Season 2 premiere.
Gaea once claimed to be Judge Dead's daughter while trying to swindle someone. In the later part of the first cycle, the human being behind Judge Dead turns out to be around the same age as her, if not slightly younger.
Fantöm's downfall, his comeback as a low-level character, his enrollment in the Noob guild, proving his innocence and revealing the identity of the guilty party are all essential to the story and need to happen as close to each other as possible. As a consequence, Season 3, the first half of the third novel and the seventh comic tell very similar stories, which disappointed fans who were attracted by the promise of seeing different adventures of the Noob guild in each media. Ironically, the parts similar to Season 3 were probably crammed into no more than half a book and one comic precisely so the completely new stuff could start showing up again as fast as possible after that single exception.
As you might guess, many expected Noob: Le Conseil des Trois Factions to have more of whatever they liked in the webseries. Since it couldn't have more of everything, there were bound to be some disappointed people.
Like You Would Really Do It: Gaea and Sparadrap getting kicked out by Judge Dead in early Season 2? Of course they were going come back one way or another. As for Master Zen, avatar banning has become a slap on the wrist by Season 3.
Fabien Fournier and other members of the Production Posse are known to be fans of their local rugby team, whose fan slogan is "Parce que Toulon" (literally "Because Toulon"). Noob fans come in two flavors regarding this: those who have appropriated the "Parce que Toulon" slogan and those who have changed it into "Parce que Noob".
People borrowing Sparadrap's "Of the dead".
Gaea's fandom acting like members of the guild of Gaea admirers, praising her as if she were a goddess and berating anyone saying anything bad about her.
Moral Event Horizon: Gaea is treated as if she crossed it in Season 4 when after losing her affiliation to the Empire because of failed quests and bad deeds, she asks to be invited into a group composed of a couple of Gaea Worshippers' guild members under the (implied) pretext of a higher probability of finishing a quest by their side, then kills Sparadrap, Ivy and Golgotha, making the Coalition her new affiliation in the process. Two episodes later, Ivy states that the act was unforgivable.
Another interpretation exists for that event but is Jossed in the fourth novel: Gaea really was The Mole for the Coalition all along, and lost her affiliation to the Empire on purpose to go back to her actual side. That interpretation stems from her affirmative answer when Gordan asks her if she's "coming home": that could either be her dropping the mask now that her former guildmates can't hear her or her playing the masquerade that ensures the Gaea worshippers' guild's faithfulness more seriously now that she's joined them. A couple of other facts were in favor of that interpretation: Golgotha saying that her cursor would "revert to its original color" if she finished a quest (the change to red was probably due to her being the guest of a Coalition group) and that Gaea was never seen choosing her faction when she created her avatar.
Popcultural Osmosis Failure: Some of the audience didn't get the reference to A Christmas Carol while watching episode 10 of Season 1 and mistook the death of Morgan Lavande (Omega Zell) shown by the ghost of Christmas future for canon, leading to some confusion when he appeared perfectly fine in episode 11. Some also assumed that Morgan's ultimate fate was shown in that episode. The death has been confirmed to be non-canon.
Rooting for the Empire: Reading the novels and likable/charismatic players may make one gain a little sympathy for the Coalition or the Order, who are pretty much villains in the webseries and comics. Siding with the protagonists will still make one do it in a literal sense.
They Wasted a Perfectly Good Plot: Fabien Fournier himself admitted things happened a little fast in Season 3 and having it covered in the first half of the third book did indeed help make things more clear. However, the plotline involving Fantöm being in the same guild as the person who blackmailed him in Season 2, an ex-colleague whose mails he wasn't answering in Season 1 and a former borderline loony fan who is now capable of speaking to him normally only got its surface scratched. For instance, his only conversations with guild members were them getting him to join, the introduction of the episode in which he was supervising their progression in a dungeon, him announcing he was going to start solo playing again once levels 91 to 100 were unlocked for the guild and him announcing he was going back to the Justice guild. The second occurrence did have Omega Zell ask Fantöm if Gaea threatened him after finding out about a plan change that seemed strange to him (but was actually Arthéon-approved), but the conversation quickly changed to Sparadrap's warrior being part of the party. There was also the group screencap in the last depicted occurrence. However, the potential of the situation still feels under-exploited, even considering that the fact it existed made Fantöm vouch for Omega Zell when he showed up on Justice guild's doorstep.
Tough Act to Follow: The webseries at least is got this even before it got finished. Fabien Fournier was originally planning to take a "Noob break" between Season 4 and 5 (e.g. late 2012 and most of 2013) in favor of producing and releasing WarpZone Project and Le blog de Gaea. A mix of this trope and Hype Backlash caused the "Noob break" to only last six months and Season 5 to have six episodes by early July 2013. In addition, there's a Broken Base about which show is best.
Pironess in The Stinger of Season 5 Episode 9. She's trying to warn whoever will listen that the world is in great danger, but the only response she gets is Meuhmeuh making fun of the Welcome to Corneria aspect of her speech. After that, he tries to kill her for apparently ignoring him.