When they are at Lucifer's hideout you can see Jackson County on the fence in the PlayStation game The Last Of Us, where the story of the game is set in an apocalyptic world and you have navigate your way through Jackson County.
When Dean looks out the window of his motel room after he's been transported to the year 2014, the movie theater sign says "NOW SHOWING: ROUTE 666". This is a reference to the episode "Route 666" in season 1. It is also a reference to the episode "Hollywood Babylon" in season 2, where the director of the haunted movie set they were hunting has a poster for the supposed movie "Route 666"
When Dean first wakes up in the future, he encounters a small girl, with her back turned to him, with a teddy bear and calls out "little girl...little girl...don't be afraid." The girl then proceeds to turn around and attack Dean, who is forced to defend himself, revealing that she is in fact infected with the Croatoan virus, which turns people into zombie like creatures. This scene closely mirrors the opening scene of "Days Gone Bye", the pilot episode for "The Walking Dead". Sheriff's Deputy Rick Grimes has just woken up to find the world he knew gone, devastated by a virus that turns people into zombies, and he comes upon a small girl with a teddy bear, with her back turned to him. He calls out "little girl...little girl...I'm a policeman, little girl...don't be afraid". The girl then turns around, revealing that she is a zombie, and attacks Rick forcing him to defend himself. Another interesting fact is this episode aired in October of 2009, exactly one year before "The Walking Dead" premiered. Series star Jensen Ackles is admittedly a huge fan of the "Walking Dead" comic series also.
"The End" is the final song on The Doors self-titled album and includes the following lyrics; "Of our elaborate plans, the end Of everything that stands, the end No safety or surprise, the end I'll never look into your eyes...again"
The trivia items below may give away important plot points.
Jensen Ackles says that playing the alternate future version of Dean was one of the most challenging versions of Dean he's done. He had to make Dean recognisable but different, all while playing present-day Dean as well. Jared Padelecki frequently says this is one of his favorite of Ackles' performances, while Ackles also frequently says that Padelecki's turn as Lucifer in the white suit is one of his favorite performances by Padelecki to date.
Dean is transported to 2014, where Castiel is no longer an angel. Season 9 was set, and aired, in 2013-14, and in it, Cas has lost his grace and is human, meaning part of the future Dean was shown was true. In this episode, Chuck Shurley also makes an appearance and, after season 5, the next time he appears is in the season 10 episode "Fan Fiction" which is also set in 2014.