Laris describes Zhaban as a "stubborn Northerner", while tapping the Romulan assassin's forehead. This may be a reference to the Romulan forehead ridges, which Zhaban has but Laris doesn't. This may be an attempt to explain why, throughout the franchise, Romulans have sometimes had ridged foreheads, and other times not. It would seem only Northerners have them. It also seems to be referring to Star Trek creator Gene Roddenberry's similar explanation for the more elaborate Klingon makeup in Star Trek: The Motion Picture (1979).
Rios mentions that he served as XO (Executive Officer) on a Starfleet ship called the ibn Majid. The ship is most likely named for Ahmad ibn Majid. He was a famous fifteenth century Arabian sailor and explorer who authored several books on oceanography and maritime navigation.
While the EMH (Emergency Medical Hologram) is treating his injured shoulder, Rios orders a bottle of liquor from the replicator, asking for "aguardiente." This Spanish word roughly translates to "burning water," and is used to refer to a number of different distilled spirits in Latin America.
Raffi's home sits in the entrance to the parking lot at Vasquez Rocks.
The title, "The End is the Beginning," strongly resembles a quote from T.S. Eliot's poem "Little Gidding" from "Four Quartets": "What we call the beginning is often the end. And to make an end is to make a beginning. The end is where we start from."