The title is a reference to the movie The Greatest Story Ever Told.
This episode has the second title that makes a reference to this movie; the other episode is "The Wettest Stories Ever Told".
Among the sites the cast visits are:
The Cenacle, the traditional site of the Last Supper
The Wailing Wall, the last remaining portion of the Second Temple (and the closest that Jews today can actually get to the Temple Mount, due to Jewish religious restrictions—fear of accidentally treading on the site of the Holy of Holies)
The Church of the Holy Sepluchre, the site of Jesus' crucifixion and burial
The Dome of the Rock, the third-holiest site in Islam (in reality, Homer and any other non-Muslim would be forbidden entrance)
The Dead Sea
The Negev Desert (no hint is given as to what the name of the desert in which Homer Simpson got lost in was, but it is generally assumed to be the Negev because it is the main desert in Israel)
The Reformers parody film parodies both the Transformers franchise and the different movements in modern Judaism (particularly the more liberal Reform branch and the conservative Orthodox branch)
In Homer's vision in the desert he sees a tomato, a carrot, cucumber. Parodies of Larry the cucumber, Bob the tomato and Laura the carrot from Veggie Tales.
The scene in Jerusalem where the man plays the violin on the roof is an illusion to the famous musical Fiddler on the Roof' about the Jewish milkman Tevye and his family.
The music played and the surrounding characters when Dorit is chasing Bart are similar to the film Run Lola Run.
Jakob tries to sell Marge his Uzi that he used to kill "three Ugandans". This is a reference to Operation Entebbe, were Israeli Commandos saved Israeli hostages that were kidnapped by Palestinian and German terrorists and their plane landed in Uganda.
Everyone saying that they are the messiah is a reference to Spartacus.
As Homer sings "I am so thirsty" in the desert, he does it to the tune of the theme song to Lawrence of Arabia.
Homer mentions stupidflanders.org. A domain lookup shows that is owned by FOX. (As of July 6, 2010, this domain name not in use.)
During the Wailing Wall tour, Bart says "Give my dad another heart attack", referencing the first time Homer got a heart attack (Homer's Triple Bypass).
In "Marge's Son's Poisoning" Marge wrote down of going to the Holyland and returning safely and this happens.
The last time Homer was sent abroad for religious reasons occurred in Missionary: Impossible, while the last time he considered himself a religious figure when he was sent abroad occurred in Kiss Kiss Bang Bangalore.
Vía Dolorosa actually means painful way in Spanish.
When Homer is first seen on the water slide, he is fully naked. But when he's seen next, he's wearing underwear.
When Jakob grabs Helen Lovejoy's lemon ice and throws it on the ground, everyone is holding a lemon ice cup. in the next scene, everyone's lemon ice cups disappear.