Gravity Falls in Rick and Morty
In the episode "Close Rick-counters of the Rick Kind", Rick opens up a bunch of portals to other dimensions. One of the portals has a mug with a question mark on it, a pen, and a notepad come out of it. In the Gravity Falls episode "Society of the Blind Eye", the episode's ending credits gag features Stan losing those three exact things, by having them get sucked into a Universe Portal.
In the episode "Big Trouble in Little Sanchez", a picture of Gravity Falls antagonist Bill Cipher can be seen on a monitor while Beth and Jerry go to counseling.
In the episode "The Rickshank Rickdemption", where Summer and Morty are brought to the Citadel of Ricks. Morty explains to Summer that this is where all the Ricks and Mortys from multiple alternate worlds hide from the Galactic Federation. While Morty tells her this, in the background for a few small frames are a pair of Morty twins, a boy, and a girl. The boy is wearing Dipper Pines's Pine Tree hat while the girl is wearing Mabel Pines's headband and hairstyle. In another frame of that scene, a Morty is seen holding a copy of a book similar to Journal 3.
In the episode "Rest and Ricklaxation", a decaying version of 8 Ball (Bill's friend from the Nightmare Realm) can be seen in the toxin tank.
In the episode "Morty's Mind Blowers", there's a room with archive of all the experiences Morty have begged Rick to remove from Morty's life. There's one blue bulb with the word "STANFORD". This is a reference to Ford Pines, one of the main characters of Gravity Falls, known as "The Author" of Journal 3. In the same shot (18:22) there is also a bulb labeled "Bill C.", which is a possible reference to Bill Cipher. Also in the opening dimension, there are statuettes of what appears to be the Truth Tortoise holding up a triangle with the All Seeing Eye. This could be a reference to the Gravity Falls character Bill Cipher, where the triangle has the same eyelashes as the character. Alex later responded it was simply the Eye of Providence and tweeted how to differentiate the two.
In the interactive game in Instagram "Rick and Morty Rickstaverse " by going in the federal prison, in a room is visible a monitor with the image of Bill Cipher and symbol of Journal 3. In the same place, but one picture below it, you can se a collection of Ricks items in a tray, next to one labeled "???", and it contains the three items Gruncle Stan loses through his portal in the episode "Society of the Blind Eye" credits.
Rick and Morty in Gravity Falls
In the real-life published version of Journal 3, which is canonically identical to the journal featured in the Gravity Falls series, there's a silhouetted Plumbus, and Zigerionon on one page (What Does It Mean?!), and in another page there's a copy of Ford's WANTED poster, with an encoded message (in made-up series cipher) on the corner reading "RICK WAS HERE". On the secondary page (My Travels), Ford mentions fistfighting with a talking chair, which might be a reference to the Furniture Universe.