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.