Artist Disillusionment: Lewis has said that he's really tired of people badgering him about "Shadow of Israphel", and that it actually demotivates him.
Colbert Bump: Moonquest brought a weird example. After Simon gave a shout out to a man on Twitter named #1 Bird Dad, said Twitter user gained thousands of new followers.
Creator Backlash: None of the people who worked on the Jaffa Factory series are really fond of the bee breeding and power supply part of it. In part 7 of MoonQuest, Simon explicitly says that once the Jaffa Cakes started being shipped onto the truck, the series after that got "really boring". They've said that if they can find a way to breathe life back into the series and freshen it up, they will, but tell us not to hold our breath. They go back to the factory in Episode 96 of Moonquest.
Mean Character, Nice Actor: It is important to note the difference between the Yogscast members themselves and the characters they play in the Tekkit series. Whilst they are to some extent playing As Themselves, there are some major changes made in order to facilitate the story. For example, there is no fierce rivalry between any members of the Yogscast. They're all friends with each other, and any "rivalries" are lighthearted and entirely for fun (or in Rythian's series, as part of his Tekkit story).
As of January 2014, all the parody music videos on all channels have been made private owing to copyright. Mirror uploads are still available, but their quality is mostly inferior and the majority are hour-long versions, "nightcore" and so on.
Old Shame: In this video, Lewis admits that he is not fond of the "Wizard Gandy" adventure map series that he and Simon Lane did, saying that it was one of the worst maps they have ever played. Sparkles*, who had that as his first video editing task at the time, also commented negatively, mentioning that he had to cut well over an hour of the duo raging. In an ironic twist, people started flooding in to watch the episode again shortly after.
Series Hiatus: The Shadow of Israphel. When the series seemed to abruptly stop putting out new episodes in the middle of season three, there were/was/is lots of speculation that it had become an Orphaned Series. Lewis has said that it simply can't be continued at the moment because of real life constraints and some of the original crew not being around anymore (not that it stopped complaining about SOI's hiatus or speculation he was lying). Every once in awhile they throw in a Shout-Out in some of their other series alluding to/joking about SOI taking so long/being constantly delayed.
Going hand-in-hand with going Off the Rails. Mr. Astley, for example, was not intended to be a creeper; the creeper had just randomly spawned in the dark basement that was meant to store the redstone mechanisms to play a noteblock rickroll as a door trigger that was never finished.
According to a Q&A with Rythian, Teep the Dinosaur was originally going to just run around and be an Easter Egg/Freeze-Frame Bonus during Rythian's Tekkit series. Then Teep killed Zoey on accident in a million-to-one chance, and from there they just decided to incorporate him into the story.
Duncan's constant giggling during his conversation with Rythian was because he couldn't stay in character, but Rythian liked how it ended up making him look like a mad scientist.
According to the wikia, Sjin and Sips tried getting Simon and Lewis' old guild member Yohi to join Sipsco, but he was away and Rythian ended up joining as an extra member of staff for their series.
The original lyrics for "Big Girl" were, according to Lewis on the 2013 Dwarven Dairy Livestream, much more offensive towards fat people than the guys deemed appropriate, and they had to get Sips to tone them down. Of course, given the internet, this may well have been for the best.
If the Twitter pages for Sparkles* and Sjin is any indication, there are a long list of parodies that will never see the light of day due to the whole copyright issue. Among these was a parody of a song from Frozen that Sjin really wanted to do. On the plus side, the copyright thing at least led to "MoonQuest".
It was ultimately inevitable considered the copious amounts of Fan Dumb, but from June 15th 2013, the comments section on the main channel, and later Rythian's, was shut off. Old videos don't seem to have been affected however. As of the end of August 2013, the comments were re-enabled.
Though, ironically the more stupid part of the fandom itself wasn't really to blame, apparently the final straw was people impersonating the Blue Xephos channel flag to steal people's personal information.