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.
Type "Ben", "The counter resets.", "Majora's Mask", "You shouldn't have done that.", or "You've met with a terrible fate, haven't you?" into Cleverbot. Go on, try it.note They don't work every single time, but they do work. You'll have a higher success rate if you start out on "Majora" or put that in front of the others.
The first time you realize that, because of the video resolution and such, the "footage" was actually created from a rom might sour your Willing Suspension of Disbelief a bit. You'll get over it quickly, though, and then there is no one to protect you anymore.
The Ryukaki arc suffers from this due to him narrating his videos to questionable effect.
During the original video (Day Four.wmv) the moments when Link is being attacked with the fire attack had me laughing. Especially when he's about to finish the Song of Time and is instantly killed.
The latest announcement, which declares that you will be notified when the game restarts, whether you have internet access or not. This was followed up when anyone who had donated (and therefore indirectly "submitted" their street address) received a typed, somewhat threatening letter in the mail accompanied by a suspiciously apropos newspaper clipping.
Which led to a different kind of Paranoia Fuel, combined with Fridge Horror, that the reason we haven't heard from the Author in so long might be because a recipient somewhere didn't realize it was part of the ARG and called the police, who traced it back to Jad and (at best) ordered a cease-and-desist... as the person who proposed the theory said, "The situation is hypothetical, but not implausible." note (Paraphrased, as the post seems to have been deleted.) It was deemed highly unlikely, but still sparked a small-scale scare. (Now try saying that ten times fast.)
Player Punch: When the ARG started back up, the players desperately tried to figure out how to save Kayd Hendricks/Ryukaki. In his last video message, he lets the players know that they were so close to figuring things out, but they were ultimately unable to save him.
"Stop Having Fun" Guys: Almost every Alternate Reality Game gets guys like this, but this one seems to be full of them: Guys with no concept of immersion who love to scream "This isn't real and you're all morons for falling for it!" at everyone, and respond to any explanations of "Yes, we know it's not real. It's a game and we're playing along." with "Well then you're even bigger morons than I thought! How can you enjoy it if you know it's not real?"
On the flipside, there are also people who take the game so seriously, anything that breaks the immersion is instantly deemed an offense. The biggest example thus far is king kong.wmv, an April Fools' Day joke vid posted on Jadusable's account. Cries of ruination resounded amongst the comments section (though they generally were in a very vocal minority).
That One Cipher: The first cipher of File 59, which currently remains unsolved.
Word of God says we're not supposed to get into the unknown stuff yet (the unsolved ciphers and the still locked files) as the keys to those things will be provided in the upcoming interactive game. We're still welcome to try, but he doubts we'll be able to pull it off without the clues from the game.
Uncanny Valley: That's most likely why Ben/Statue!Link creeps Jadusable out so much.
The Woobie: Poor Jadusable, all he wanted was a little nostalgia...