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.
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.
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.
Because of weather conditions, entry 66 was put off a week.
Trolling Creator: Tim Sutton on tumblr. 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.