Pilot (aka Emotions in Motion) - S1-E1
Visible crew/equipment: In the scene outside of the Rialto, where Dawson is scolding Joey for being rude to Jen, Joey's shirt is falling off one shoulder. She shrugs to fix it, and her shirt lifts in the back, exposing her mic. (00:31:50)
Pilot (aka Emotions in Motion) - S1-E1
Visible crew/equipment: It's morning at Jen's and Grams'. Jen is seated at the kitchen table downstage/far left. Grams is upstage/right at the stove scrambling eggs. Grams crosses downstage to put the eggs in front of Jen and the mic overhead upstage/right peeks out just a tiny bit. Grams crosses back to the stove. Suddenly the microphone - including the rod the mic is on - just drops down almost completely into the frame over Grams' head and is not pulled back up.
Kiss (aka A Prelude to a Kiss) - S1-E3
Visible crew/equipment: When Joey, Bessie, and Bodie are at the seaside restaurant talking about how large Bessie looks (during her pregnancy), you can see a boom microphone dipping in and out of the picture above Bessie's head. (00:07:40)
Baby (aka Look Who's Talking) - S1-E6
Visible crew/equipment: When Pacey is telling Tamara they should go out together there is grass on the camera lens, in the bottom center, in each shot of Pacey. (00:05:05)
Visible crew/equipment: When Joey is in Dawson's room, trying to tell him about her relationship with Pacey, she can't find the words and turns to leave. As she bends over to climb back out of his bedroom window, you can suddenly see a microphone wire protruding from the back of her white shirt. It's a visible vertical line, and as she continues to climb out the window, you can see that there is no mike pack on her lower back. (00:19:05)
Visible crew/equipment: When Joey is walking out to the pier to talk to Dawson, right after the wedding; the wind is blowing her dress back and you can see a prominent, solid line going up the front of her dress from about the waist up to the neck. I assume this is probably a microphone wire of some kind and not just a wrinkle, as the line is solid and protruding through the material.
Coming Home - S4-E1
Visible crew/equipment: In the very beginning, when Joey and Pacey are on the boat Coming Home, there are a few closeups of Pacey that show a small microphone jutting out the material of his shirt, right under his collar. (00:01:05)
Coming Home - S4-E1
Visible crew/equipment: In the scene where Joey and Pacey have arrived back at Capeside, and are getting things ready to get off the "True Love," in one shot you can see the microphone clipped to the back of Joey's shorts.
Answer: It's the same apartment Joey had in NYC. Comparing it to the beginning of the Finale; you can tell it's exactly the same location, furnishings, Plasma TV etc. Apparently Chris was only living with her at HER apartment, and now Pacey has taken his place at the end. I guess this implies Pacey successfully started his own restaurant business in NYC as he had dreamed, to be with Joey.