DEAN: Tomorrow you start paying. Bye. [leaves]
LORELAI: Bye. And then there were three.
A reference to the American counting game, originally called “Ten Little N*iggers”, and later “Ten Little Indians”, and now “Ten Little Soldiers”. A standard of black and white minstrel shows, the original title was used for a 1939 mystery novel by Agatha Christie, now less controversially called And Then There Were None. In the novel, a series of ten murders are planned to fit with the structure of the original black and white minstrel rhyme; the pertinent line is, “Four little n*gger boys going out to sea, a red herring swallowed one, and then there were three”.
Lorelai may be thinking of the 1978 album … And Then There Were Three, by English rock band Genesis. The title was chosen because it was the first one they released as a trio, following the departure of their guitarist. It reached #3 in the UK and #14 in the US. Its most successful single was Follow You Follow Me, which coincidentally or not, is a title vaguely reminiscent of Where You Lead (I Will Follow), the theme song of Gilmore Girls.
The Annotated Gilmore Girls 