Richard Hatch gets compared to Darth Vader twice, once during the show, and once during the Reunion. During the show, they even dub the infamous breathing sounds over a shot of him with a black fishing mask on.
The Immunity Challenge in Episode 12 (the one where Rudy repeatedly exclaims "I Dunno") was obviously an Homage to The Blair Witch Project
The monkey that lives nearby the Chuay Gahn camp during Thailand is referred to as Magilla by everyone.
The Amazon:
Ryan Aiken, the first contestant booted off of the Amazon season, makes a shout out to the John Woo film Hard Target when voting for Roger.
When Rob C. votes out Roger, he does a radio announcer impression, then proceeds to sing "Kiss Him Goodbye" by the band Steam.
Jonny Fairplay performed Shout Outs to various WWE wrestlers during his Tribal Council votes.
All-Stars had one episode where Amber mimics a famous scene from Basic Instinct.
Commenting on Colby's status as The Ace being called into question, James compares him to "Superman in a fat suit."
In the double elimination episode, when the villains have to stop eating and vacate tribal council, James points and laughs, reminiscent of Nelson Munz from The Simpsons.
In the final ten tribal from Caramoan, Malcolm likens his outcast trio to the "¡Three Amigos!."
Reed's jury speech from San Juan Del Sur uses metaphor to compare Missy to the Wicked Stepmother from Cinderella.
The majority alliance from Heroes vs. Healers vs. Hustlers calls themselves ''The Round Table."
Rick Devens has a confessional in Edge of Extinction where he compared his vigor to the Kool-Aid Man, wanting to "bust through the wall shouting, 'Oh yeah!'"