Chris Carter had to lobby hard for the casting of Brad Dourif as serial killer Luther Lee Boggs. Dourif was more expensive than the usual guest star but Carter knew he would be perfect for the role. He rang Fox president Peter Roth at his home on Thanksgiving to plead his case. Roth agreed to it, mainly because he wanted to get back to his dinner.
Mulder addresses Scully as "Dana" while inquiring as to her well-being in their first scene. Presumably, because he heard of her father's death. She hesitates and mouths her name to herself before responding "fine". The agents had been exclusively on "last name basis" up until this point.
Part of this episode was filmed in Vancouver. After her first meeting with Boggs, Scully is driving back to the hotel and sees the "angel of stone." This is a WWI memorial piece called the "Angel of Victory" located at Waterfront Station.
The version of Beyond the Sea that we can listen to in this episode is Bobby Darin's. Glen Morgan's parents were huge fans of him and named Glen's brother, possibly the best writer of The X Files, after him.
While the series is known for its alien storylines and mutant stand-alone stories, it has also dealt extensively in the area of seemingly ordinary serial killers. "Beyond the Sea" is the first episode to reflect that.
After writing Humbug, Darin Morgan seemed to be dissatisfied with his work, so, in order to write his next script, Clyde Bruckman Final Repose, he reviewed Beyond the Sea in order to catch up with what the series was about.
In this episode we can see how different is Scully's home layout from how it is in the last seasons. The door is in the opposite side of the kitchen among other details. In The X-Files: Tooms (1994) we could see that the bathroom also is different, and in The X-Files: Duane Barry (1994) and The X-Files: Ascension (1994) clearly we could see she lives in a low floor. It's even plausible that she moved to an upper floor after the first seasons, as far that we can see that they use the stairs when they go out from there.
The trivia items below may give away important plot points.
This could be the only time in the entire series in which we can probably see Scully's little brother, Charles, and probably his kids and wife. In the funeral Maggie Scully says that her father only wanted his family there and we can see besides them two men, two women, and two kids, who could be Bill, Melissa, Charles and his family.