Clue 1: Who drinks the water I shall give him, says the Lord, will have a spring inside him welling up for eternal life. Let them bring me to your holy mountain in the place where you dwell. Across the desert and through the mountain to the Canyon of the Crescent Moon, to the Temple where the cup that holds the blood of Jesus Christ resides forever.
In The Last Crusade, Indy first travels to Venice to meet up with a colleague of his Father's, where they discover clues to the location of the holy grail (and have a good ol' fashioned boat chase)
Clue 2: Hey, you can't steal that! We already did!
This doesn't refer to Indy, but rather the
Horses of Saint Mark, which were originally from Constantinople and stolen by Venice after the Sack of Constantinople. Napoleon then in turn stole them from Venice in 1797, but they were returned in 1815 (hence the 'you can't steal that!')
Clue 3: When a wife looks like that and her husband's so fat, that's immoral. When she kisses that jerk while I do all the work, that's im...
This is a reference to the scene at the end of the Simpsons episode
The Italian Bob, where Marge and Homer are enjoying a gondola ride through Venice and the gondolier is singing the clue to the tune of
That's Amore