When Roz talks about cloning a sheep, she's referring to Dolly, a sheep that was born as the result of cloning at the University of Edinburgh in Scotland in 1996.
The Act 2, Scene 2 title card, "The Ego Has Landed," is a play on the phrase "The Eagle has landed," which was uttered by astronaut Neil Armstrong when his Apollo 11 lunar module Eagle landed on the moon on July 20, 1969.
Frasier (Kelsey Grammer) makes a big deal in this episode about being pursued by two women: he explains that he wants to enjoy this now that the day has finally come. However, 'Three Dates and a Breakup (1997)' - one of the final episodes of Season 4 -involved Frasier being pursued by not two but three women. He made a very big deal about that as well.
In the final scene, Frasier (Kelsey Grammer) arrives at Niles' (David Hyde Pierce) apartment fresh from his date and asks how it went with Maris. Niles says that he returned the gifts (plural). Since Frasier wore the cufflinks on his date, the most Niles could have returned was the pocket watch.