Plot hole: When Jen is helping Dawson at the Video Store, and spots Pacey and Joey out on the street, she asks, "Dawson, do you have one of those little signs that says 'Back in 5'?" Dawson then relies "Yeah", implying he could leave the store for several minutes on a small break. But then he and Jen follow to where Joey and Pacey are taking their dance lesson. Dawson then proceeds to dance his way through an entire dance lesson, witness a confrontational scene in the coat closet, and then lingers outside in the street having a meaningful conversation with Joey. This would all obviously take up a considerable amount of time, much more than a small break. Therefore - how would he have gotten away with closing down the Video Store for that amount of time without losing business and possibly his job? Especially if the sign only indicated he would be away a few minutes. This would be very un-Dawson-like to be that irresponsible with his only place of employment.
Plot hole: When Jack and Andie are using the computer at school, Jack shows a clear knowledge of computers by explaining search engine criteria to Andie. It's also mentioned that they had already done an extensive background check on Ben, again implying that Jack has extensive computer skills. So why would Jack, who is apparently quite skilled with computers: not know what an Instant Message is, not know how to 'get rid of this thing' by clicking off the IM window, and not know to click 'Send' in order to send an IM back to Ben. It doesn't make sense that Jack would know so much about computers, and not have any awareness of how something as simple and basic in Internet usage as 'Instant Messages' would work.
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.