The scene in the Prophet recreated Saratoga corridor from Emissary:
TACTICAL: But this is your existence.
SISKO: But it's difficult to be here, more difficult than any other memory.
SISKO: Because, because this was the day that I lost Jennifer. I don't want to be here.
JENNIFER: Then why do you exist here?
SISKO: I don't understand.
JENNIFER: You exist here.
As someone who has lost quite a few friends and relatives along the way, this is the scene that resonates the most for me from all of Trek.
I just watched Emissary this last weekend and the more I see this episode, the more I think it might be the best pilot. You get so much out of each viewing and the scene you mentioned, BillJ, was terrific. He was teaching the prophets about Linear time and the Prophets were teaching him to not grieve anymore and move on. It was a really poignant scene and beautifully executed.