Being Watched: Jadusable starts feeling like this not long after he gets the game.
Bloodless Carnage: Even though the story is really terrifying, the videos are all shot within the engine of Majora's Mask, an E rated game.
Surprisingly, at 4:42 in Jadusable.wmv, Link suffers an instant death as a blood splatter appears on the screen. Truth is, Ocarina and Majora both had blood for when you got hit, but was so unrealistic looking (though it was indeed red) that the games got an E-rating anyway.
Body Horror: Jadusable's dream. Also, although a less bloody version than usual for this, Link's "glitched" back.
Creepy Child: The Elegy of Emptiness statue. And to a lesser extent, BEN... Or whatever is calling itself BEN...
Dead Person Conversation: Possible subversion. At first you think the chat messages with BEN are this, but then it turns out BEN may not be, well, BEN, after all.
Defictionalization: A rare collaborative and (mostly) non-deliberate example. After reading thetruth.rtf, hordes of people started inputting BEN-related questions and answers into Cleverbot, effectively training it to play the role of BEN when prompted.
Development Hell: And HOW. For starters, the real trailer to the game was supposed to come out on May 10th. Overall, due to development issues and financial setbacks, this trope applies.
Gaslighting: Mentioned in passing in thetruth.rtf. BEN thinks it would have been hilarious to just randomly close a window or move the mouse a little bit occasionally and wait for Jadusable to notice.
Get Out: The first time the Wayward Horizon was broken into, someone cut off the Welcome Post by Guide to tell us in Binary that we shouldn't be in there, and to GET. OUT. Minutes later, another thread is posted, this one by Kelbris, simply saying "GET OUT" after which the password was changed.
Haunted House: Reversing the reversed portions of Ryukaki's final video (so that they play normally) will reveal that he has been living in Ben's old house all this time.
Irony: The reverse Song of Healing is notoriously creepy and unsettling, especially in the context of the story and videos. But what do you get when you play the Song of Healing backwards in the actual game? Saria's Song, one of the most upbeat tunes in the series.
Nor is this, if Jadusable's youtube channel is a reliable source. Or not...
Word of God says any information that isn't found here or here is not to be accepted as clues or evidence. Theories are welcome, but nothing outside of those two locations is to be taken as official (presumably with the exception of the Ryukaki arc).
Nightmare Sequence: Jadusable has one of these later on where the moon children from Majora's Mask, who BEN has apparently been removing any reference to up to this point, slowly sew his arms and legs together and a mask to his face, making him resemble an Elegy statue.
Nothing Is Scarier: All BEN does is make vague threats, and mess with his computer. It's surprisingly creepy, and it leads to a horrifying nightmare sequence.
Off the Rails: To the point that gamejacking attempts eventually contributed to tighter moderation.
There is a fic called the Orchard of Love that features KaydXBike, BENXBike, and KelbrisXBEN action.
Schmuck Bait: Thetruth.txt wasn't posted to 4chan, but to a file sharing service as an .rtf file by BEN, so he can get you, too.
Schedule Slip: The ARG was apparently supposed to conclude (or have something important happen) on 4/23. Due to Jadusable's coding buddy being busy with work, it (and the rest of the third arc) got delayed.
Shout-Out: The name on Ifrit/Matt's Gmail account was "Matt HUBRIS", the capitalization on the name possibly being a subtle shout out to Everyman HYBRID.
There seem to be a few for either adaptation of The Shining. The whole "Link Statue following you" thing seems to be based on the hedge animals that follow that story's protagonist, Danny. Then there's the line "Come play with us..."
Un-Cancelled: Jadusable announced that due to low funds, he would not be making any more chapters of Ben Drowned. Two days later he announced that he had gotten such an overwhelming amount of donations that he would in fact be able to continue after all.
No, it most certainly will not. The latest series of events are the chronicles of one Ryukaki, who was originally One of Us and was simply following the ARG until shit literally got real (at least according to his first video).
A Wizard Did It: The haunted Majora's Mask game is obviously being played on a modern computer and being modified through Gameshark codes instead of a capture from an N64. Understandable, though, since actually modding a Majora's Mask cartridge would take a ridiculously long amount of time and effort. The in-story explanation? BEN did it.
Word of God: Jadusable did a long blog post (found here) about the plot, and revealed a few things with this. First of all, the whole ARG is parallel to the plot of Majora's Mask. A creature trapped inside a (cartridge/mask) uses someone else to help it escape into the (world/internet), and a bold hero from another dimension (Link/Alex) must save us. Oh wait, Alex is dead.
Someone on 4chan also theorized that Jadusable's the moon, though it makes much more sense to say that he is, in fact, the Skull Kid, as he's suckered into something that could destroy everything by accident. Also, Alex is back.
Jadusable held a Q&A on Feb. 16th answering some burning questions such as what mhftt stands for. Matt Hubris Four Two Three. Most questions were met with noncommittal responses or a Shrug of God, though. Transcribed here.