After Hours - S5-E21
Audio problem: Just after Audrey storms out of Pacey's apartment, after catching him with Alex; Pacey runs after her and they begin arguing in the street. Audrey makes a comment that 'it meant your arms around her, and HER tongue down YOUR throat' referring to The Kiss between Pacey and Alex. But then Pacey counters with 'well actually, it was HER tongue down MY throat' in sort of a comic way, as if he was correcting a backwards situation. But Audrey had just said the same thing! One of the Actors messed up their lines, probably Busy Phillips since Joshua Jackson seemed to have his lines correctly.
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.