When Jen comes through Dawson's bedroom window (near the end), a GhostFace mask from the "Scream" series can be seen on the shelf Dawson uses for his movie props. One of the "Creek" creators, Kevin Williamson was the independent writer of the original "Scream." It's even plausible that this is an actual mask from the movie.
During the narrative for this episode, Paul Stupin talks about the town of Wilmington, NC where Dawson's Creek was filmed. Wilmington is such an old town, that every building has one ghost or another, and every one has a ghost story. There is an inn there called the "Wilmingtonian" where they all would stay while filming. This is a very old inn, and the room behind the front desk was supposedly haunted. One of the writers stayed there, and would be woken up in the middle of the night with the hairs on her neck standing straight out and she would sense a presence. Another writer who stayed in that room supposedly saw a figure in the mirror. There is also a restaurant in Wilmington where a waitress claims that once when she was working on the upper floor, she turned around and saw an apparition standing out on the balcony. It was a fellow dressed as a soldier.
Paul Stupin mentions this true story while discussing the show during the narrative for this episode. Once when Joshua Jackson (who played Pacey) was out swimming at night, there was a girl who was caught in some currents. He jumped in the water, swam out and brought the girl to safety. Joshua made the local newspapers as a "hero", and was known around Wilmington as 'the guy who saved the drowning girl'. The show also had a big ceremony on the set, where they gave Joshua a life preserver in honor of his heroic deeds.
There was an alternate scene filmed for the Pilot Presentation, where Tamara is first introduced in the Video Store with Pacey and Dawson. In this alternate scene; the location was an actual Video Store located in Southport, about 50 miles away from Wilmington, NC. They decided to reshoot the scene using a smaller Video Store in Wilmington that didn't look like a chain. Once the show was picked up for a Series, they needed a Video Store location that they could use easily every week. Also, in the alternate scene Tamara is wearing a more conservative outfit of black that covered her quite a bit. They put her in a much sexier dress for the aired version. Tamara's wardrobe and the location were changed to give a better tone to the show.
When Dawson walks into Mr. Gold's film class, he passes by a large movie poster on the wall by the door. This is the movie poster for the film "I Know What You Did Last Summer," which had the screenplay written by Kevin Williamson, Writer and Creator of "Dawson's Creek."
The scene where Jen is in Dawson's bedroom for the first time and Gram's calls for her, the woman standing in the doorway was not Mary Beth Piel. She was a stand-in, as they hadn't cast that character when the scene was shot. This is also evident in the scene where Dawson and Jen are standing outside of Jen's house after their "date".
When Joey and Dawson are talking before they leave on their respective trips, Joey makes a comment about getting it right "in another life when we are both cats". This line was also made famous by Penelope Cruz in the movie "Vanilla Sky", starring her and Tom Cruise. Ironically, Katie Holmes is now married to Tom Cruise; and in the beginning of the Vanilla Sky movie when he is running through Times Square he goes by a large poster of none other than Katie Holmes. Bit of a coincidence?
In this scene; when Pacey, Dawson and Joey are in the car driving back from the hospital, they aren't actually driving. This scene was filmed using something called a "Poor Man's Process"; which involved shaking the car a little, and a crew person holding two lights behind them to simulate headlights. This scene was actually shot on a soundstage, and could be fit in easily at virtually any point in the filming schedule. Normally scenes like this are shot with a car being towed on a trailer, but in this case that method was too expensive for their TV budget.
Originally, they were thinking of actually moving the show "Dawson's Creek" to another city in order to send off the main characters to Boston for College, etc. Cities considered as locations for College, etc. were Montreal, Vancouver, Baltimore, Austin, and San Diego. Baltimore ended up being the easiest city to 'fake as Boston'. But ultimately it was decided that it was simply too expensive to move the show; so they ended up sending their main characters to Boston, but actually keeping the show in Wilmington, NC and filming there during the 'College Years'.
Generally with Dawson's Creek, the scripts were generated in LA and sent down to Wilmington, NC about 7 days before filming. The director for that episode arrived at that time also, to prep the script. But during Season 2, they were so concerned about making the dialogue perfect the scripts starting showing up later and later to the point where sometimes they arrived only hours before shooting. Needless to say, the actors were becoming upset as they didn't have time to prepare properly and the director had to prep off of an outline. Fortunately, they resolved the problems and they didn't repeat themselves during Season 3.
Because the weather was so bad, and it was raining for days, they had to keep putting off filming the Graduation scenes. The opening scene in this episode, the Practice Graduation was shot either the last day or the second to last day of filming because of the rain. All week long, the weather was awful and kept raining, which forced them to delay the Graduation scenes.
During the narrative for this episode, Kevin Williamson mentions that the show "Dawson's Creek" was originally written for North Carolina. Because they didn't want a Southern show, they came up with Cape Cod area outside of Boston. But during the Winter episodes, it's hard to get snow in the water in the real location of Wilmington, NC.
When they are filming Natasha's scene, there is a close-up of the marker board. You can read the film title "Wicked Dead", the Director's name "TODD" and on the bottom line, the name "Frank Perl for "Camera". This is obviously an inside joke, as Frank Perl was the Director of Photography for Dawson's Creek.