Jenny says that she hasn't been into mortal danger since the events of "The Dark Age" and that Rupert has been trying to find out if she's ok ever since. Also Cordelia refers to Rupert's secret that came out in "The Dark Age".
Giles states, "And the rest is silence." This seems to be a reference to the movie, as it was the last words Merrick, Buffy's first watcher, left with Buffy. The phrase in the movie would later become relevant to Buffy in her defeating Lothos.