- This is the first appearance of Ms. Choksondik.
- Mr. Mackey has many lines in this episode, but he says "mmkay" only once.
- This episode heralds the first major change in the opening sequence - after starting off with the original segment of various pieces of scenery and character coming in from off-screen, the words "4TH GRADE" burst out of the ground, and the new sequences begin. The new sequence included an updated theme song, 3D computer generated models of the four main characters (and Timmy for some reason), promises of updated walk cycles and more explosions, and various clips of previous episodes were in the background throughout. This intro was used until the Season Five episode "Kenny Dies".
- This is also, to date, the only time the theme song's "style" has changed and Kenny's lines haven't - the other two changes, in seasons six (where Kenny was absent) and eleven, have both involved Kenny's line changing too.
- This episode references a "Geek Debate" attempting to determine how many episodes of Star Trek exist. The debate centers on the status of the episode "The Menagerie".
- In this episode only, Ms. Choksondik speaks in a British-like accent, despite coming from Denver. It's possible that she might originally be from the United Kingdom, but has lived in Denver for sometime.
- It is strange that Kenny laughs at Stan's alteration to Ms. Choksondik's name (Ms. Makesmesick) and not her actual name, given his perverted sense of humor.
- The two geeks are based on the sound people who work on the show.
- The episode parodies The Empire Strikes Back with Mr. Garrison acting like Yoda while training Ms. Choksondik how to handle the children. Mr. Garrison even speaks in a Yoda-like voice for a moment.
- Timmy, whose vocabulary has previously appeared to be restricted to his own name, in this episode manages to expand his vocabulary to "Please help me!"
- The geek's room is littered with aliens from other episodes; including a toy Marklar as well as a poster of the South Park alien and Spooky Fish on their door.
- For once, Mr. Mackey has to go to someone else for help with counseling - he called Chef in for help with Principal Victoria.
- Cartman says "Ha ha, charade you are" to Mrs. Choksondik, a reference to Pink Floyd's song Pigs (Three Different Ones). This is the second time he cites this song, first in "Cat Orgy" and third and final time in "Scott Tenorman Must Die".
- The situation with Timmy unable to stop the wheelchair or get off it is a parody of the movie Speed, The 5 mph reference may be a nod at an episode of the popular Irish/UK comedy Father Ted.
- The duck taped to the microwave is possibly a reference to The Brave Little Toaster Goes to Mars.
- When the two geeks talk about the number of episodes in Star Trek they switch between 72 episodes but then they say there are 73 episodes, and back to 72. Either way they would be wrong - there were actually 79 plus a pilot that went unaired until 1988.
- Although Principal Victoria says that Mr. Garrison hasn't been seen since the last school year, he can be seen in a pew at the South Park church behind a man behind Ms. Cartman in "Do the Handicapped Go to Hell?".
- There is a poster on the geeks wall which says Lena, an obvious parody of Xena.
- This episode hints at the possibility that Stan is aware of Kenny's tendency to die. However, this was disproven in "Mysterion Rises".
- A poster of the alien in the beginning of the episode "Spookyfish" is seen on the Star Trek geek's door.
- The obese Star Trek geek resembles Edgar Jomfru from Metalocalypse.
- Cartman previously asked Mr. Garrison "How would you like to suck my balls?" in South Park: Bigger, Longer & Uncut, however, he did not reply "present them" at that instance.
- When the class enters the fourth grade classroom for the first time, Token Black appears to be walking off the ground and in front of Craig Tucker for a few seconds.
- There is a picture of Kathie Lee Gifford on a bookshelf in Principal Victoria's office.
- The blond-haired geek claims there are 72 Star Trek episodes at the scene where Kenny tries to rescue Timmy and brown-haired geek says there are 73. But when the boys go back to the geeks' houses to ask them to build another time machine, they have reversed their positions. While at the brown-haired geek's house he says he doesn't want to live in a world with 72 (ST:TOS) episodes, which contradicts what he said seconds earlier. This may not be a goof at all, but intentionally done to parody Star Trek fandom since their argument was whether there were 78, 79 or 80 episodes.
Kenny is put onto a relay, which rolls down the road straight on at Timmy's out of control wheelchair. While trying to cut the wires on Timmy's wheelchair, Kenny misses the wheelchair and goes straight past it. Kenny hit a pothole, and flipped over onto his face. He says "I'm okay", then suddenly gets jerked back. His face gets dragged along the road, killing him. Stan comments sarcastically: "Well, who didn't see that coming?"
In a later scene directly, after Cartman says: "Au revoir, teacher", Kenny is sitting next to Stan in the class again. He is seen up until one of the nerds yells: "I'll kill you!" In the next scene, Kenny is nowhere to be found.
The hidden visitor is seen when Cartman is singing about third grade; the flashback of them in the classroom has the usual "OUR PETS" noticeboard, but with a drawing of a Visitor's face.