When Luke is leaving Lorelai messages on her answering machine, he states his phone number is (860) 294-1986. This phone number actually goes to "Luke's" real-life brother-in-law, George Dover, who is the Director of the Children's and Maternal Hospital at Hopkins in Baltimore. People who call "Luke" reach George, who then asks for a donation to the children's hospital.
The song Rory picks to be her and Dean's song, "Candy Man", is from the movie "Willy Wonka and the Chocolate Factory". This was the movie that the two watched on their first date when Lorelai invited Dean to movie night.
The episode title is a reference to the Henry James novella 'Daisy Miller' in which a young American woman vacations in Europe, but whose flirtatious nature gets her into trouble. Rory also says "Say goodbye to Daisy Miller" in a conversation with Lorelai.
When Lindsay answers Dean's phone, she very easily could have seen who was calling by looking at the caller id. When Dean first gave her the number in a previous episode, Rory stated they would now be saved to each other's contact list.