So, this wiki is a bit unusual in that it doesn't use the word "canon". It recognizes only official material, but never says whether it's canon, non-canon, or up to us to decide. So, anypony who wants to discuss canon can come here!
(Unless you're an anon after July 1st, in which case you can say your comments on GameTalk X.0 which doesn't even require email address, just username and password each time you make a post)
I questioned this episode's canonocity because in it, Fluttershy gets over her fear of dragons, and Rainbow Dash gets a fear of dragons. Yet in Dragon Quest, Fluttershy and Rainbow Dash have traded back their roles. However, the "hop skip and jump" thing from this episode is referenced in Feeling Pinkie Keen so it must be canon. We'll just say Rainbow Dash got over it and Fluttershy is like Ron Stoppable who gets over his fear of monkeys how many times?
Some consider episodes by Merriweather Williams non-canon because they dislike her episodes, especially The Mysterious Mare Do Well with arrogant portrayal of Rainbow Dash. But she made up for it in Wonderbolts Academy, I never had anything against her episodes, and I see dislike of a writer no reason to view episodes as non-canon. (plus, she wrote the episode where Rarity bites Fluttershy's tail for the first time and I've been waiting for her to bite a tail, until that episode she was the only one of the mane 6 not to... moving on.)
Andy Price has said we choose for ourselves whether the comics are canon, so it's basically a matter of headcanon.
The first arc, The Return of Queen Chrysalis, retcons Chrysalis's presumed death in A Canterlot Wedding by giving her Team Rocket immunity to survive the fall and brings her back with an evil plan to kidnap the Cutie Mark Crusaders and drain Twilight's magic. The second arc has the revival of Nightmare Moon to possess Rarity.
Now, I noticed a kind of different style to the comics, plus being IDW with different writers which I usually count as non-canon they kinda didn't feel too canon to me, but I tried to think of them as canon so Chrysalis could get an official death scene - until she survived her duel with Twilight. As cool as it would be to have Chrysalis be tormented by the Cutie Mark Crusaders even worse than Fluttershy in Stare Master, appearances by Mola Ram and Pennywise, or to have Rarity possessed and Spike kill Nightmare Moon the second time, I just want Chrysalis dead so badly (both because she's an uber malevolent and menacing villain and because of what she did to Twilight in ACW Part 1), so I decided comics are non-canon and she fell to her doom in ACW. But that's just my opinions. (you might say that's ridiculous but I wasn't the least bit disappointed to Discord turning good)
However the Nightmare Moon arc might have a few plot holes in it. Up until then, Screwball viewed comics as canon despite disappointment about the Chrysalis thing. a.) Why is Luna's mane and tail the same way as after being released from Nightmare Moon's control? Her transformation in Issue 8 suggests it happened before Luna Eclipsed, but it has to be after Magic Duel because Trixie is good and talks about getting a second chance. b.) Spike's Fire Ruby, doesn't Rarity have it now? c.) While not a plot hole just yet, it was kinda risky to their "making them fit in" depicting the enemy that created Nightmare Moon, when the show's writers have said there is an outside force behind her and Discord, and I don't think the Nightmare Forces were involved with Discord. So what happens when the show reveals the enemy behind them?
So, for the time being the comics will still be like Dragonball Z movies to me: I still watch/read them and enjoy them but to me they're non-canon. Of course any of you can count them canon if you want, and come up with explanations for the Nightmare Moon plot holes.
A lot of people didn't want it to be canon because of the human ponies. It's said it will have no effect on the show so it probably won't be referenced in Season 4, or with any Flash Sentry or Sunset Shimmer. Now, not a lot of people seem to care because they thought the movie was either all right or, in some cases (including Screwball) awesome, with cameos and references making up for the human ponies and high school theme that everypony predicted would be awful.
But there is one plot hole I heard of. At the end of Magical Mystery Cure, Twilight can fly effortlessly with her wings, the way she flies at the screen from the distance of Canterlot. But I heard in Equestria Girls she can't fly. Why? Is this the work of the No Reason?
EDIT: It could just be that she can't fly when she's nervous. She seemed confident at the end of MMC, but was clearly nervous about the princess summit, and remember Fluttershy in Dragonshy
Also, if Magical Mystery Cure is the first of a "three-parter", then aren't the first two episodes of Season 4 set directly after? Unless Equestria Girls is set after them.
Twilight Sparkle and the Crystal Heart Spell
Or whatever that book's called. It sees the return of Gilda, acting as antagonist alongside Trixie, who turned good before Twilight became an alicorn. For that reason, I consider the book non-canon. It'd be like if Babs returned in a later episode and returns to bullying the Cutie Mark Crusaders, which didn't happen because she's still friendly with Apple Bloom when she returns in Apple Family Reunion.
I know some might argue Silver Spoon seems to turn good in Family Appreciation Day while returning to bullying in One Bad Apple, but maybe either Diamond Tiara convinced her to go back to her side, or else One Bad Apple is set before Family Appreciation Day.
Season 3 and above
Anypony who hasn't left the fandom either likes or doesn't mind Season 3, or else hates it and might be willing to FanonDiscontinuity it, on account of Lauren Faust not being involved anymore, departure from her style, and disliking most episodes. Me, I'll always go by Season 3 as canon (King Sombra, for pony's sake! say what you want but he was darkest villain and his death was so awesome!) and hope to see more of Discord, Trixie, of course Luna (who appears in more episodes this season than Seasons 1 or 2), and am looking forward to more Alicorn Twilight in Season 4 so we can see what regular episodes are like with her as an alicorn.
Although I might sound like a hypocrite if I decide to FanonDiscontinuity Season 4 if they bring back Chrysalis and turn her good. I don't mind it happening in fanfiction but in canon I don't want Chrysalis to depart from her "pure evil" and, again, want her dead so badly. (although a return and a disintegration would be all right) Or if they have Rarity not appear... I could go on about how I think she might be written out due to her role diminishing after Episode 36 and not getting her own episode in Season 3, but this isn't the place.