The Unova Arc was the longest arc pre-GC, and it dragged on for about a month and a half before the group finally decided that enough was enough and did a Time Skip.
The GC Arc, as mentioned before, was even longer.
PMD-R has gained this reputation as well, going on for over four months (over 1000 pages)
It was immediately followed by Kanjoh-2, which went on for a bit over seven months.
Since Unova-2, Arcs have been generally expected to go at least 3 months, though it's generally been longer since Kalos.
RtAU was in the background with no resolution until the Re:Glitch finale finally gave a real showdown against the Seven Jerk Dragons. Whether the rest will be picked back up is still uncertain.
Hoenn-2 lasted about a year with Re: Glitch going on a bit longer than that.
Archive Panic: The RP has been around since February 2011 and has averaged something between 4000 and 5000 pages each year. Efforts have been made to try to lessen the panic by linking to important posts on the wiki's Archive pages, however, but that's still a work in progress.
Big-Lipped Alligator Moment: Several back when this thread was in Forum Games, mainly due to random people who don't want to participate in the arcs showing up and doing stand-alones. Highlights include:
Kyurem accidentally calling DS' Xtransceiver. (one has to wonder who it was really trying to call...) Somewhat subverted later on when this leads to the discovery that only those who have Minds of Crystal are capable of understanding Kyurem's speech.
Zeal's April Fools Day 2014 posts, introducing several characters and concepts out of the blue and not having referred to them since.
Continuity Lockout: The RP's heavy continuity and sheer length can make it a bit difficult for newer people trying to get into the loop, especially during a plot-heavy arc, but the RP generally tries to be welcoming to people when they join. Efforts have also been made to try making continuity easier to grasp using the wiki.
Die for Our Ship: Quite a few in-universe fanfic writers had this in mind when shipping the trainers.
While inside 'M's organic core, DS has to hold Anom's hand in order to help him get through it without freaking out. One of the first things that seem to come to Anom's mind about this is "I hope Wolf doesn't misinterpret this." Later on, Anom and Wolf get heart swapped by a Manaphy at the beginning of the Oblivia arc. Not wanting to tell the others, they decide to pretend to be each other. This leads to some interactions between Anom-pretending-to-be-Wolf and DS that cause the real Wolf to essentially become jealous of himself.
Cilan dyed Anom's hair green at one point early on in the Unova arc. And as mentioned above, Anom later ended up switching bodies with Wolf, who has green hair.
A lot of meta-conversations and in-RP conversations have subjects that become this trope later on.
Some of the events back during the Unova arc seems to predict some of the things that would later be revealed to be part of the plot in Pokémon Black 2 and White 2, such as Ghetsis taking control of Kyurem.
Zero remarks here about Dittos having twins. Later, Straw meets Eskay's Ditto, Doopliss, who looks exactly like Straw in human form, only with a goatee.
During the Pokésona Arc, Mendel's Initial Persona Pythagoras envelops Mendel while in use and shares a similar design to Futuba Sakura's Initial Persona Necronomicon, which wasn't planned at all by virtue of being designed before Futaba's reveal.
This trope has happened so much that it has achieved memetic Running Gag status with a lot of the playerbase with the phrase "The Game Freak Spy strikes again!" when the games or anime features elements that have a strong resemblance to characters, places, items, or concepts that have been part of the RP for a while (and sometimes years).
Thanks to the multitudes of Media Arcs and Shout Outs the RP has had over the years, the phrase 'We have a [X Video game company] spy too' or, 'Apparently the Game Freak Spy works for [X Video game company] too' has started to be used when elements in RP show up in non-Pokémon franchises.
Herbert and Duke's bromance has many, many of these moments. Duke thinks of Herbert as a little brother and Herbert himself thinks of him as a big brother, even if he's not as likely to say that out loud, but he often acts as if he has a crush on his "big brother". Made more obvious by the scene where Herbert was upset with Duke because he likedLyurimore than him, which sounds awkward even in context.
When Mira the Mienfoo first meets DS and her team, and witnesses Artemis the Liepard fight off a Beartic, Artemis has Bishie Sparkle from Mira's point of view. Artemis later sees Mira the same way after Mira evolves into Mienshao.
When DS is trying to figure out her feelings after Wolf kisses her Mira talks about how one sometimes have to deal with discovering feelings one has never felt before when they meet someone special. While Mira is talking about this, she's staring at Artemis.
Marceline the Gardevoir had a kinda Precocious Crush (It's complicated...) on Lily the Lilligant almost since she evolved into a Kirlia, which was at some point reciprocated.
Psyche had three ships sailing with her within her first few weeks of joining, one of those three Eskay x Psyche became canon.
Skye has also become one, having various ships with several others, notably, Luke, Caliburn, and Diane, the last of the three eventually becoming canon.
Lucius, as a new PC, had already gained three ships: Herbert x 'Sarah', Herbert x Sakura, and Herbert x Carol. Later, Crewe X Herbert also became a thing. To say nothing of his Ho Yay with Sam and Joseph...
Crewe has an incredibly good name for Portmanteau Ship Names; Crab, Craw, Crowe, Cruke, Crouch, Creddler, Mewe, Craisy, Cryche, Viewe, Crewebert, Creskay, Skewe, Criane, Crent...
Lake, who after all is a mon on his own and has defeated Red twice. Since he's his own mon now, he can also speak in the discussion thread. And in the PEFE Chatroom, where he is the most badass (and adorable) creature imaginable, capable of using Judgment among other equally incredibly and fictonal attacks.
Mike the Techie. He's basically the WAAPT equivalent of Chuck Norris now.
Daisy didn't realize that Josie the Medicham was male. To be fair, 'Josie' is a rather feminine name.
Happens again, this time with Virizion. The Mysterious Old Man claimed that it is male, but after an extensive debate between everyone, a verdict was found and now Virizion has been decided to be female.
Pentigan's Pokémon form is a Lopunny.
Most of the team was confused as to whether Mezzo was a boy or girl when she first joined. During the GC Arc, she invoked this in the fanbase by making contradictory claims about her gender.
Carl (A male Panpour) tries to avert this by not evolving.