The hidden tapes are any tapes in MarbleHornets of which Jay does not truly know their origin. 'enttry #37' and Entry ###### are the only two uploaded without Jay's permission and Entry #29 shows a video Jay can't seem to recognize, and doesn't know the cameraman of that episode. 'entry' was uploaded by Hoody. Jay has since then unlisted the video (it can still be found if you have the link), but decided to incorporate it into Entry #61.
Since these videos are incomprehensible at best, the videos do not have a specific timeline in which they occur, as they all are random. Entry ###### could have been any time, enttry #37 is clearly footage of childhood (effectively making it the oldest tape), and Entry #29 shows NOENTRY.avi which is the only one that can be cataloged. Based on the bloody evidence at the scene, NOENTRY.avi takes place between Entry #49 and Entry #50.
enttry #37 seems to be of Alex's birthday, and the audio is slightly warped. During the first seconds of the tape, the Operator Symbol appears over Alex's face, most likely symbolizing that the Operator has been stalking Alex since he was a child. When "Alex" blows out the candles, the video cuts to a man in a suit walking in what seems to be night.
'entry', unlike the others, was a message from Hoody. It is clearly presented to Jay as a means to tell him Tim is in trouble.
In Entry #66, Jay finds a tape that Hoody might have left at the abandoned hospital. At first, it did not play at all, due to dirt being inside the tape. However, Jay has since gotten it to work. It contains footage of Hoody stalking Alex through the Hospital, and knocking him out.
'entry #73' seems to have been uploaded by Hoody without Jay's consent. Tim confirmed so on the MarbleHornets twitter page. In the video itself, Hoody finds a tape in Tim's living room, but is forced to leave without it due to Alex awakening.
In Entry #75, Jay and Tim go to Tim's house to find Alex, but Jay wants to find the tape. After failing to find it in the living room, he angrily asks Tim for it. When Tim refuses to admit that he has it, Jay takes it from him. Tim warns Jay that the time is not right to watch the tape, but Jay ignores him and storms out. The tape is revealed to show what happened to Jessica after Entry #32. Tim later tells Jay that he has had the tape ever since they woke up in the shack in Entry #62.