Chuck's pseudonym "Carver Edlund" is a combination of the names of the executive producer and co-producer, Jeremy Carver and Ben Edlund.
The diner Dean and Sam eat at is called Kripke's Hollow Diner - named for the series creator, Eric Kripke.
Chuck asks the brothers if they really had to live through the "bugs" and "the ghost ship" and apologizes for the bad writing of those chapters. Actual episodes Bugs (2005) and Red Sky at Morning (2007) (which featured a ghost ship) are widely considered by fans to be amongst the worst in the entire series.
When Chuck states that writing himself into his books as a prophet is like "M. Night level douchiness," he is referring to director M. Night Shyamalan, who regularly appears in his own movies.
Chuck, thinking that Sam and Dean are his fans, asks them if this is "a Misery thing". This refers to Stephen King's book (and later movie) of the same name where a writer's "biggest fan" kidnaps him and restrains him in her house and forces him to write another book of his finished series.