Blooper: The initial upload of "enttry" #37 had a kid wearing a Spongebob Squarepants t-shirt in 1991, Spongebob didn't premiere until 8 years later. The second upload edited out those shots.
In entry 60.5, as Jay is going through Tim's medical documents, one of them lists symptoms of headaches and insomnia, along with a third one apparently blacked out in marker. However, since the pages were wet, the ink leaked through onto the next page, revealing that the third symptom - whatever it is - was never written on the page to begin with.
Genius Ditz: he has proven multiple times to be very good with electronics
The Danza: Tim, Jessica, Brian and Seth. Brian is actually a double example: Alex's Marble Hornets film features a character named Brian played by a character named Brian...played by a man named Brian. Oddly enough, Jay and Alex themselves don't follow this trope (their real names are Troy and Joseph), nor do Sarah and Amy. Jessica is a happy accident, that the character was named Jessica before they hired an actress named Jessica.
Played straight in Entry #71, which takes place seven years in the past.
Fan Nickname: The Fanbase is fond of giving affectionate nicknames to characters. Slendy for the Operator, Masky for the masked man, Hoody for the man with the hood and the black ski mask, Skully for the figure with the skull mask in Entry #26 and so on. The man who Alex kills in Entry #49 is known as "Beardy" or "Bruce" depending on who you ask.
Beardy Mc Whiteshirt!
Tothe<location> has become something of a memetic phrase. It began when some commentators started referring to Masky as "Tothearby's", due to his actor gaining some weight between the seasons. This meme was reinforced in this video when Joseph(Alex)'s dog talks about going To. The. Park.
The three creators themselves have collectively been given various nicknames throughout the fandom, some of the most frequent of which are Trosephim and the Bro Trinity.
Ho Yay: the creators have A LOT of moments ,most of it is aimed at Brian
One of Us: In the DVD commentary, Troy makes a reference to Dawson Casting - among other references that both he and Tim make to nerdy activities such as surfing 4chan and playing on his NES.
Schedule Slip: Some of the later entries in Season 2 were victim of this. Troy would announce release dates for certain entries, but due to problems uploading the files he'd put off releasing them till the next day. Kind of immersion-breaking when he'd post as Jay on the Twitter page, saying he was having 'compression' problems with Youtube.
Word of God says that the shadow 'reaching into Alex's head' at the end of Entry #22 was a happy accident (the original plan was to simply have a shadow pass over him).
Seth wasn't in the original script, but his girlfriend (who played Sarah) asked for him to be included, Troy and Joseph wrote him in as the cameraman for the student film. Slight case of Ascended Extra, as he came back later as the only survivor of the student film aside from Alex. Which doesn't last.
Tim's line in Entry #9 about Alex spending too much money on tapes was improvised by Tim Sutton himself.
Trolling Creator: A lot of responses about the ending of the series are very troll-ish. The creators refuse to confirm how the Operator costume was made and performed, if Hoody/Brian was indeed totheark, or what the ark itself actually is.
Tim's Tumblr is very much this. Pretty much constantly. Expect about two-thirds of the questions he's been asked regarding the series to be answered with "Meth," "Brian," or "You can't tell me what to do," and other equally obtuse variations.
What Could Have Been: The Season 2 DVD has an unused version of Entry #37 that would have re-introduced the Operator back into the story earlier than it did. However, Troy and Joseph felt the entry was weak and conflicting with what was going on, so they dumped it in favor of the VHS-flavored enttry #37.
While the broader brushstrokes for the final entry had been worked out years in advance, the finer details were apparently tweaked. For example, they didn't originally plan on ending with a driving shot, and Jessica was originally going to be working at the antique store from the start of the season. They also toyed with the idea of Jay surviving through till the end.
Skully, the skull-faced Masked figure who appeared briefly in Entry #26, was originally just added in as a result of Rule of Cool. However, during season 3, the creators toyed with the idea of him being Jay's Masky-esque, Operator-induced alter-ego, like Masky and Hoody were for Tim and Brian, and Jay himself would discover this through found footage. It was ultimately scrapped, though the creators have suggested the idea he could still be lurking around somewhere.
Word of God: Mostly subverted during the first year while the identity of the cast and production team was still secret, but since revealing themselves, Troy, Joseph and Tim have done a large number of interviews and convention panels about the behind-the-scenes workings of the series. They even have an official podcast.