1) Preston Northwest had his memeory erased by the Society of the Blind Eye, along with Pacifica Northwest.
2) Mrs. Gleeful's Mind wa erased as well, which means that her husband may have been the one to do it, perhaps because she discovered the Society of the Blind Eye
3) Mabel was the one who taught Soos how to open the vending machine (in the past), and he was the one who taught her (present time)
4) Soos has a band-aid on his emergency salami
5) the scredriver Dipper dropped in Blendin's Game was the object that caused Soos to work for Grunkle Stan
6) When the kids first enter Stan's secret lab, you can see a six-fingered handprint on the wall. A clue that this is related to the author (Not What He Seems)
7) In episode 10, season 1, at 00:00:05 one of the arcade games has a green Bill Cipher on it. In the same episode, there is a parody of Pac-Man, and Pac-Man is a yellow triangle.
8) In the same episode, the show "Why you ackin' so cray-cray" says MT instead of TM
9) The fallen "S" fell in the third episode.
10) Mabel and Dipper's heads are biger than their torso.
11) Blubbs and Bellingham dressed up as each other for Summerween.
12) The carpet in the mystery shack has a picture of Bill Cipher on it
13)Wendy reads a magazine called "Avoid Eyecontact (Monthly)"
14) Soos's WiFi password is Fixinit2 which is an an anagram of Xfinity2, also meant to be "fixing it," perfect for a handyman
15) "I only cry in the rain, so my tears can't been seen." -Robbie
16) Robbie has spray-painted "Die, Dipper die" on his wall.