Within the episode Zoey (who is married to the Captain) answers her phone by saying 'Ahoy'. It is implied that the captain makes her say this, however, Alexander Graham Bell (the man who patented the telephone) originally suggested that people answer the telephone by saying 'Ahoy'
When Barney says: "Manatees City, where the grass ain't green and the girls ain't pretty" is a reference to Guns N' Roses song "Paradise City"
After The Captain knocks Ted's phone into the ocean he says "Can you hear me now?", a reference to the Verizon commercial.
When Marshall realized "The Mermaid Theory" is true and sees his secretary, Iris, as a Mermaid, instead of a Manatee, the song that plays is Ariel''s theme from The Little Mermaid (1989), which is also the verse section of the main song called "Part of Your World".
When Marshall realized "The Mermaid Theory" is true and sees his secretary, Iris, as a Mermaid, instead of a Manatee, the song that plays is Jodi Benson's theme from The Little Mermaid (1989), which is also the verse section of the main song called "Part of Your World".