These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Here's one that can be made entirely by accident. Towards the end of the series, Kyle Hebert's beard became noticeably white, creating continuity errors. However, one could argue that Wario knows that the battle is coming and is gradually becoming more and more nervous.
This claim could also be offered for Link.
When confronted in the alley way Luigi sees a baseball bat on the ground and uses it during the short battle. Soon after Lucas and Ness appear, the latter of whom isn't carrying around his trademark bat.
When Link talks to Luigi about Dedede's murder, he mentions that forensics found bits of skull like what would be the result of getting hit in the head with blunt force trauma. This doesn't get mentioned further, and Luigi notably leaves it out while trying to profile the killer, but remember, Ness uses a baseball bat...
This is because someone at The Escapist screwed up and forgot that the series was granted exception to the "no F bombs" rule that the site has.
Harsher in Hindsight: Knowing what happened to Mercer, Ganondorf's breakdown and death in the finale is very uncomforatable to watch.
During the final battle, Pit's wings are ripped off. In Kid Icarus Uprising, Pit's wings are burned off for flying too long, though unlike in Brawl he gets them back.
Hilarious in Hindsight: It is mentioned that in the news extras hosted by Lakitu that Mario nearly beat Tom Nook to death. As of November 2011, PETA is complaining that Mario is skinning Tanukis and wearing their skin.
Ho Yay: Lots, the series ships Ike/Marth and Falcon/Pit, among others.
Les Yay: There also seems to be something between Samus and Barbara the Bat. It was originally believed to be just the product of Samus's flirtatious attitude in Episode 3, but they're seen holding hands, comforting each other at Red's funeral service, so there may be something to it.
Hype Backlash: The Escapist held an event where members of their website would receive an award if they watched all nine available episodes in the week leading up to the finale in order to hype up the release of the final episode. The episode was eventually posted two weeks later, because The Escapist hadn't consulted with the producers on how long it would take them to edit the final episode, and suddenly announced it a week earlier than planned.
See also Executive Meddling for details. The guy's been on bed rest for a while. He damn near killed himself trying to edit the final episode by himself.
"The trophy gallery", when it's finally revealed what happened to the murder victims after their insides were left behind: they were stuffed, crudely stitched back together, and put on display.The worst was probably Peach, which was somehow rigged to stand up and spill blood out her mouth.
There are some especially gruesome scenes in the finale, such as Pit's wings getting ripped off, and Kirby taking a bite out of Luigi's face.
Ship Tease: YMMV, but throughout the entire show, Samus implied to have a thing for Luigi as well as Barbara the Bat. To go for the hat trick, she also flirted with Trainer Red even though she knew he was in a relationship with Leaf.
Special Effects Failure: While most of the costumes and choreography is really good for a webshow, there are a a fair number of awkward moments. Most noticeable, however, is the Donkey Kong costume.
The mouth on the actor playing Dedede is clearly visible while he's talking. This isn't helped by the fact the beak doesn't always move properly.
In Episode Eight, Link's sheath visibly flaps limply against his arm as he stands up after being knocked.
Link's ear prostethics are obviously not part of his normal ears.
Jigglypuff killing Wario in the finale. Sure the former is, in real life, a plush toy, but that doesn't excuse the fact that the scene looks really silly.
Squick: The series is FILLED with this, and there's something here for everyone:
King Dedede's comment to the stripper Malon: "You're on stage soon, go get Epona." Malon does not look very enthusiastic about this. Given the state of everything else, sure Epona may not be a horse, but that doesn't change the Unfortunate Implications of the line...
And the "Trophy Gallery". Dear God in Heaven, the Trophy Gallery!
Ganondorf bleeding from everywhere under the kids' influence, and then later his head being chopped off after already having been stabbed by a sword.
The final few moments, where it is HEAVILY implied that Kirby killed and ate Ness. How is it implied? Kirby is wearing a very familiar looking bloody baseball cap - just like he would be in Super Smash Bros if he'd swallowed Ness and copied his powers.
Tear Jerker: Red's death, and the song he plays in the same episode. Hell, the entire ending of Episode 9.
Think about this one for a bit, and realise this is the biggest Player Punch the series throws. Narrative-wise, it has no reason to happen. It makes Wario and Ganondorf out as horrible, horrible people, that couldn't possibly be redeemed. ...Except they were already there. If Red didn't die, chances are the rest of the series would have played out exactly the same. ...Well, minus the Rest attack.
Red controlled the Pokemon, and as Samus points out, is thus in the safest place in the city. Ganondorf and Wario were just taking out another potential threat, the target was the Pokemon more than Red.
Not to mention the flashback right after the final battle, where Luigi remembers the very start of all the chaos, the day the whole mess began. They were still happy and still friends, even though some of them knew the horrors that were about to begin. "This is the last great moment of this kingdom," says Peach wistfully.
Surprisingly, the scene showing Wario taking care of Waluigi. Despite who he is, he still shows that he cares for someone.