When in the bar, Charles points out a criminal he brought in earlier named Isaac. Isaac (Joe Monde) is the same criminal Jake used as an informant in the episode Charges and Specs (2014).
Ozeroff's home is the same apartment used in Scrubs (2001) for JD and Turk's shared apartment. Incidentally, both Scrubs and Brooklyn Nine Nine feature lead characters involved an almost symbiotic (and often-times awkwardly close) bromance. Turk & JD's apartment was a renovated room in an old hospital in which Scrubs was filmed. Ozeroff's apartment was just a similar-looking set.
When Jake and Stevie are in the supply room, Stevie "Donkey Kong" punched Jake, who then says "it's on". This is a reference to the saying "It's on like Donkey Kong"
When Jake, Stevie, and Charles go to the perp's apartment, Jake says that either the perp was a drug dealer or Nic Cage was his interior designer. Andy Samberg played Nicholas Cage on Saturday Night Live.
Stevie calls Charles "Earl" and he responds "You know my name is Charles!", a play on the TV show My Name Is Earl (2005).