Rick eating ramen noodles in his killing spree montage is a reference to Rick Deckard eating in a Japanese noodle bar in Blade Runner (1982).
Rick pops up on screen impersonating Stan Lee's various cameos in Marvel movies or in comic books where the editor explains when previous events occurred.
The whole layout of the Citadel of Ricks with the domes on outriggers, as well as the Mortyburg dome decoupling and drifting away into an uncertain future, is a reference to Silent Running (1972).
When Morty asks the bar keeper for a rum and coke and he says, "What are you 20?" Twenty is the legal drinking age in Japan.