When Minister Ahkna is asked to leave at the start of the episode Crichton is heard saying: See you later, sweetheart. This is because Minister Ahkna is played by Ben Browder's real life wife, Francesca Buller.
When John says, "If it were done when 'tis done, t'were best it were done quickly," he is paraphrasing one of the most famous and revealing soliloquies in William Shakespeare's 'Macbeth'. In Act I Scene VII of the play, Macbeth is meditating on whether to go through with his (and his wife's) plan to murder Duncan, the king. John's decision mirror's Macbeth's.
The 4th season trilogy "We're so Screwed" is known by the individual episode titles: "Fetal Attraction"; "Hot to Katratzi" and "La Bomba" in the UK. The UK didn't approve of the trilogy title.
The messages "Hi THERE" (and "DEAR JOHN" which appears in the following episode) attached to the nuclear bombs are references to Stanley Kubrick's Dr. Strangelove or: How I Learned to Stop Worrying and Love the Bomb (1964).