The character of Joey is inspired by Fannie Norwood, a long-time friend of Kevin Williamson. According to Williamson: "If Fannie watches, she will know exactly where I got some stuff. It's nice because only she will know."
There are a few references to Tom Cruise in the early seasons. Joey and Dawson is watching a scene from Jerry Maguire. Later, during a suspension from school, Pacey is seen watching Jerry Maguire. Pacey and the mysterious Eve (Jen's half-sister) convince Dawson to let them use his house for a Risky Business-inspired fundraiser to pay for a boat mishap Eve led him into. Katie Holmes (having had a relationship with Joshua Jackson during the series) later became Mrs. Tom Cruise number 3.
Meredith Monroe's character, Andie McPhee, left the series in November 2000 almost halfway through the 4th Season. Her name remained in the opening credits until the end of that season, even though she wasn't in any of those episodes.
In season one, episode seven - 'Detention' Dawson compares the group's Saturday detention to the film, 'The Breakfast Club.' He mentions the cast are now languishing in TV obscurity. Pacey then mentions Emilio Estevez from the film, saying 'he was in those duck movies, remember? God those were classics. So funny.' Joshua Jackson was in fact in 'The Mighty Ducks' with Emilio Estevez.
Dawson's creek was actually written about a small place on North Carolina coast and most cities referenced are in that area. However, due to its location, TV officials deemed it was unspectacular to use it as the setting for the show because it's a very sparsely populated area.
The trivia item below may give away important plot points.
Abby's Morgan's death happened after Monica Keena requested her character to be written out of the series, as her boyfriend at the time was living in New York and she didn't like being in Wilmington, North Carolina, where the show filmed.