The song that plays as Alan and Denny fly over Canada is "Oh, Canada" by Five Iron Frenzy. Although here it is trimmed out, the full song mentions that William Shatner is a citizen of Canada.
In the episode "Finding Nimmo" there is a reference to William Shatner's career in Star Trek. While resting in the cabin, Alan Shore (James Spader) mentions to Denny (Shatner) that there are parasites called "Cling ons". Denny reacts with a shocked look and says "Did you say Klingons?" There are also other references to Star Trek in other episodes. Some examples being Denny's cell phone and a metal detector making the communicator chirp and Denny saying "What am I supposed to do, beam to Boston everyday?"
While in the Canadian courtroom, Alan tells the judge they will leave him with two small but lasting words. Then Denny says, "Denny Crane, eh?" Denny making fun of Canadian accents is especially amusing when one considers that William Shatner was born in Canada.