Milhouse insists that his use of the word "radical" is a defining characteristic of his, but throughout the series he has never been heard saying the word at any point other than his complaint about the Shelbyvillian kid using it.
A boy who looks like the Black Weasel is seen in Bart's class.
After Nelson bursts into the classroom, all of Bart's classmates run out to learn what has happened. However, only a few of them really follow Nelson.
Todd Flanders runs with the boys to lemon tree. It means that he must in Bart's class when Nelson runs in. However, Todd is supposed to be either home schooled or at a Christian school. He could have joined them as they were on their way to the Lemon Tree.
When Bart assembles the boys and tells them how it went, he forgets to tell Database about his role.
Bart mentions Springfield has many angel sightings. There was a angel skeleton discovered in Lisa the Skeptic. "Lisa the Skeptic" was released several years after Lemon of Troy, so the line about angel sightings is not a reference.
In the end when the Shelbyvillians drink turnip juice, it looks somewhat the same as in Springfield (old man near the vegetable/fruit).
If you look behind the boys when they enter Shelbyville, you can see two girls flying a kite at the border, one of whom is Lisa. The other is Samantha Stankey, Milhouse's ex lover from the episode "Bart's Friend Falls in Love."
After Bart labels Todd the "Quiet religious guy who ends up going crazy," Todd can be seen looking at the camera nervously.
The episode's title is a reference to Helen of Troy, the daughter of Zeus and Leda considered to be the most beautiful woman in the world according to Ancient Greek mythology.
When Shelby calls Bart a garbage man, Bart responds, "I know you are, but what am I?" This is a reference to Pee-wee's Big Adventure. This would be reused in Treehouse of Horror IX.
When Milhouse makes peace with his Shelbyville namesake, he says, "So this is what it feels like when doves cry," which is a reference to the song "When Doves Cry" by Prince.
Bart's plan to have the Shelbyvillians tow Ned's RV into the impound lot is reminiscent of the Trojan Horse strategy by which the Greeks defeated Troy in the Trojan War. In fact, when sneaking out of the RV, Homer stated, "No one inhistory has ever done anything this clever!"
Bart's successful escape from the tiger pit by adding up the Roman numerals in which he states it is Rocky VII: Adrian's Revenge is highly improbable, considering in the most recent film Rocky Balboa that Rocky is left a widower in the wake of Adrian's death in the interim period between the fifth and sixth films. There is now a seventh movie out called Creed released in 2015.
While undercover, Bart is asked by two Shelbyvillian boys on how come he isn't seen at their school. One boy asks him what is"Two plus two," Bart answers, "Five," which convinces the boy. This is a reference to the work 1984, and when Winston Smith was forced to accept the concept.
Bart trying to fly using aerosol cans is a reference to the TV show My Secret Identity.
When Bart tries to use the spray cans to escape, he sprays green color on his lower legs and feet, but when he sneaks away after distracting the boys, the color is gone. After snatching the skateboard, the color is back but after that it's gone for good for the remaining episode.
When the Shelbyville kids advance on Bart, there is a frame where two moments of their arms' motion overlap. This creates the illusion that they have two arms on each side of their bodies.
When Martin said, "A car impound lot," the subtitles on the Season 6 DVD say it was Ralph Wiggum who said it, although he didn't go into Shelbyville with Bart.