Why were the comments enabled for a short while on Entry #####? At first you'd think it's a slip up on the part of the creators, but because Jay didn't upload the video (As far as we can tell), he couldn't have disabled them until he found the video.
"Do I help or do I kill?" was referring to Alex's drawings in entry #46.
Possibly unintentional but even more awesome if so: the name Jessica means 'one who sees/beholds/seeks out' depending on what source you're using. All of these readily apply to the character. Jessica has had dreams where she was a little kid and something was watching her. To behold is also to sense. She comes and talks to Jay about the batshit insanity around them - she seeks him. See probably refers to the Operator at some point since she's been memory wiped.
We all like to get on Jay's case for being Genre Blind and going into Brian's house during the night. However, one has to remember, since no one was living there, and he already knew Brian was long gone, Jay was technically breaking-and-entering. Horrific story about Eldritch Abominations aside, he's still got to worry about the law too.
And one has to consider that the video was uploaded in the middle of winter. It was dark, but it may well have been as early as 5:00 or even 4:30.
It's always been thought that Alex was pissed at Jay for leading the Operator to him, but later it's kinda conflicted by the fact Alex seems to go looking for him. Who's Alex mad about that Jay led to him? The Maskies. Alex wasn't looking for his girlfriend, he was looking for a way to get the Masked men off his back...
The time between the end of Seasons 2 and 3 was significantly shorter than it was between Seasons 1 and 2, and it was still marked by occasional updates from Jay via Twitter. At first, it may just seem to be the result of a more polished and efficient production schedule, if we go out-of-universe. However, at the same time, it also shows that Jay is learning. Last time he went completely dark, he ended up losing seven months of time and then had to spend half a year piecing it all together again. This time, Jay only went dark for as long as he needed to. He left Twitter updates detailing a few small finds, and fully resurfaced after finally hit some pay dirt when he spoke to Tim directly. He may not be the sharpest knife in the drawer, but Jay certainly learns from his mistakes.
The operator symbol seems to come from a symbol that film operators use that appear for one frame when it is time to switch reels in old cinemas. Seen in Inglourious Basterds and Fight Club.
One can often wonder how Jay gets around seeing as he has a car, stays in hotels often after his apartment is burnt down and probably pays some sort of phone bill yet doesn't have a job. Then remember that he's a YouTube partner.
So the whole series takes place in Alabama, right? Now, what does the flag of Alabama look like? A red X.
In entry #9, children can be heard in the background of the park, and Alex even complains about them ruining the sound of the shot. Then the camera turns off for a second, Alex freaks out about it being off...and the sound of kids has completely disappeared. Now think about one of Slendy's canonical preferences for victims...
As noted on the main page, Alex's dog is mentioned in Entry #2, and never mentioned again. However, in the often overlooked Entry #15, Tim mentions Brian finding dead animals in his front yard. When Jay asks whether or not was somebody's pets, Tim changes the subject and tells him to talk to Brian about it.
Considering who turned out to be Masky, it opens up a whole new realm of possibilities on who put the dead animals in the yard.
enttry #37 is already scary enough, being an old video of Alex on his birthday with the requisite audio and visual distortion and an appearance by our friend, the Operator, but then you realize what this implies: Alex may have been stalked by the Operator long before Marble Hornets.
Don't forget though, one factor of the Slender Man mythos is that he stalks children. Alex probably didn't notice he was being followed until he started making Marble Hornets.
Enttry. Ent being a tree based monster, and "try" being pronounced as tree. Guess who shows up.
The spelling is also remarkably similar to how Jay was typing before he passed out. What if he did upload the video and has no memory of doing so? And what else could he have done in such a state that he doesn't remember?
enttry #37 is also notable for another reason: after Alex blows the candles out on his birthday cake, the dates and times in the upper right corner of the video wildly change. As was noted here, the dates all correspond to something related to death and violence.
Even better, in Indicator we see a twisted little baby doll with the 0 key in its eye. Perhaps an idication that the Operator has seen them since they were children?
In Entry 3, Alex is seen tearing up paper and setting it aside while sitting on his couch. In Entry 16, Jay finds an overturned couch in the same color, paper scraps littering the floor all around. Was he the one sleeping in the closet in that house? Was he already insane that soon into this?
Entry 26 can be seen in a completely different light considering the evidence from later entries that Alex's descent into madness may have been going on longer than we thought. We see evidence in Entry 51 that Alex may have led Brian and Tim to the Operator to begin with. Now, go back to Entry 26 and wonder why Alex is so calm and rational.
All the way back in Entry 16 Jay found (among other things) a bullet casing when searching through where Alex had lived. Due to the other events of both season 1 and season 2 this is quickly forgotten. however in entry 52 Alex pulls a gun on Jay and Jessica and is about to kill them to "tie up loose ends". Seeing as it is now all but confirmed that Alex is working for the Operator, one wonders how many other times he had to "tie up loose ends".
One of the reasons Alex was furious with Jay was for showing the videos to the world. This chewing-out occurred the day before Entry #27. Jay has just spent nearly an entire year posting even more videos, and seriously incriminating ones for Alex at that. If he was pissed enough back then to try and kill Jay...one wonders what he might be thinking now.
On a related note to above, since all of the TOTHEARK messages took place after entry #52, some of the messages they contain become far more sinister. Fragments says "you are Broken" and "you cannot be fixed". As chronologically this is the first thing TOTHEARK relays to Jay after #52 when he was attacked by the Operator and Mind Raped this raises the question of what the hell actually happened to Jay.
There was a hospital that dealt with pediatrics, among other things... near Rosswood Park. One can only imagine what the Operator did with the place - or, more accurately, the people associated with it - given the mythos. Brr.
Several observant viewers have noted that the box on Tim's bedside table in Entry 61 contains (in addition to the empty pill bottle) a razor blade. Now think back to what Tim's medical records said about suicide risk....
In Entry 70, the Operator is a lot shorter than in the other entries. Doesn't seem remarkable at first, but keep in mind that this entry takes place way back when Alex was still shooting his movie. The Operator is growing! In Entry 86, Tim tells Alex that his actions have been "feeding it". Watch the entries which are chronologically set during the student film. The Operator stands around looking scary, messes with Alex's personality, and at one point makes him bleed. The fun stuff, like teleportation, distortion of time and space itself, and distortion enough to outright break the cameras, doesn't happen until the series starts.
Quite a few viewers noticed in Entry #77 that Tim had a lot of gas cans in his garage, and quickly recalled Jay's apartment burning down.