In the hospital, the mental patients each start mumbling the phrase "What's the frequency?" This is an obvious reference to the infamous event, in 1986, where CBS Newsman Dan Rather was accosted by (then) unknown assailants. One of the assailants, apparently deranged, kept repeating the question "Kenneth, what is the frequency?" (which meant absolutely nothing to Dan Rather)
Spike's intended gift for Buffy is the same box of chocolates with which he practiced his lines on (and bludgeoned) the Buffy mannequin in Triangle (2001).
The 12th or 13th episode of each season is traditionally when Buffy celebrates her birthday; her birthday takes place in episode 13 of season 2 (Surprise (1998)), episode 12 of season 3 (Helpless (1999)), episode 12 of season 4 (A New Man (2000)), and episode 14 of season 6 (Older and Far Away (2002)).
When Dawn gets upset with Joyce and Buffy in her bedroom she shouts: "Get out. Get out! Get out! Get out!" She shouts the same thing, in the same place, in Older and Far Away (2002), during Buffy's 21st birthday.
As Dawn put the pieces together about her identity as the Key, it flashes archive footage from episodes Listening to Fear (2000), Real Me (2000), and Shadow (2000).