In the beginning, after Crichton says, "Previously on Farscape," they show few frames from each and every episode of Farscape, all 87 episodes.
John says, "Dear God, don't let me screw this up." That is a polite paraphrase of the famous 'astronaut's prayer' attributed to Alan Shepard, the first American man in space.
This is the first episode in which Moya is able to Starburst to a specific location rather than a random or semi-random one. This is inconsistent with all prior episodes, but remains the norm throughout the following Farscape: The Peacekeeper Wars (2004) TV miniseries/movie.
Last show of the series.
When Crichton blows Sikozu and Scorpius out of the airlock, Sikozu yells "Weak Species!" That is the same insult her alternate-reality counterpart yelled before trying to kill John in Unrealized Reality (2002), perhaps implying that the two characters might not be all that different.