The idea for Sisko to slowly undress as the episode progresses was director Victor Lobl's, who saw it as serving a double function; on the one hand, Sisko loosening and removing his clothing was simply to convey the passage of time as he paced around the room, on the other it was a thematic metaphor for how, as Sisko narrates his log, he is literally baring his soul.
This is listed as one of the "Ten Essential Episodes" of Star Trek: Deep Space Nine (1993) in the 2008 reference book "Star Trek 101" by Paula M. Block and Terry J. Erdmann.
In The Pale Moonlight is considered by many to be the darkest Star Trek episode ever, and more importantly, the one that challenges Gene Roddenberry's vision of a peaceful human future more than any other episode. It's exactly for this reason why many fans consider it Star Trek's finest hour.
Vreenak is on his way back from Soukara when he diverts to Deep Space 9. Soukara is the planet visited by Jadzia Dax and Worf to rendezvous with the Cardassian double-agent Lasaran in Change of Heart (1998).
According to Ronald D. Moore, the title of the episode was a reference to the phrase "Have you ever danced with the devil in the pale moonlight?" from the film Batman (1989).