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 Rickshank Rickdemption", 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.
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 are a silhouetted Plumbus, Zigerion, and a Cthulhu on one page, and in another page there a copy of Ford's WANTED poster, with an encoded message on the corner reading "RICK WAS HERE". There is also a page where Ford mentions fighting a talking couch, which might be a reference to the Furniture Universe.