Plan 9 Comics is clearly a reference to the infamous movie Plan 9 from Outer Space, popularly believed to be the worst movie ever made.
When Comic Book Guy is demonstrating the soda-resistant properties of Radioactive Man #1000, the "lesser comics" to which he refers appear to be issues of the comic that started the career of Simpsons creator Matt Groening, Life in Hell (as evidenced by Binky, the star of Life in Hell, standing on a stage on the cover). The logo of Matt Groening's comic book publishing company, Bongo Comics, can be seen at the head of the cover, in place of a title, despite the fact that Life in Hell has never been published by Bongo Comics. This could suggest that the "lesser comics" line actually refers to all of Groening's comics.
The name of the comic book hero, "Biclops," is a pun on the name of the X-Man "Cyclops".
One of the Star Wars memorabilia that Martin Prince owned was a film reel that contained an alternate ending where Luke's father was revealed to be Chewbacca, referring to the secrecy of the plot twist that Darth Vader was Luke's father and the production team even tacking on some alternate dialogue to suggest someone else is Luke's father (e.g., Obi-Wan Kenobi) in order to ensure that Vader's identity as Luke's father isn't leaked.
Bart's Transformer transforms into an ax. This may be a reference to the 80' version of Megatron which transformed into a gun.
The events of Homer Simpson's first life-long ban were a reference to Gallagher's Sledge-O-Matic stunt (which Homer ruined by eating the watermelon).
Tom Savani's diembodied hand look similar to Thing from The Addams Family.
In the same video, Steve, the military officer detailing the defense plan, also referred to the president, although the holder of the president wasn't made clear other than the use of monochrome television making it very likely to either be Harry Truman, Dwight D. Eisenhower, or John F. Kennedy.
The title of this episode refers to Comic Book Guy's catchphrase: "Worst (Noun) Ever!"
The commentary for the episode reveals it was originally titled "The Fiver", a reference to a scene in the episode. However, the scene was removed from the episode and so the title was changed.
The people on the Banned for Life wall along with Bart and Milhouse are: Nelson Muntz, Sideshow Bob (odd, considering that Sideshow Bob isn't the type who would read -- much less enjoy -- comic books, as he's into more highbrow culture), and a bearded man who looks like Simpsons show creator Matt Groening. Given how often Springfielders run into each other, and how seriously Comic Book Guy takes comments about comic books, it's possible Sideshow Bob and Comic Book Guy had met and the former insulted Comic Book Guy's favorite comics, resulting in his banning. It's also possible that he attempted to commit some crime that bothered Comic Book Guy.
The Star Wars memorabilia that Mrs. Prince planned to sell before Bart and Milhouse talked her out of it was a handwritten script for "Star Wars" by George Lucas, Princess Leia's anti-jiggle breast tape, and a film reel labelled "Alternate Ending: Luke's Father is Chewbacca."
It is revealed in this episode that Milhouse wears another type of underwear. This one with the "My Little Pony" title on the top of the rear-end of the underpants along with a picture of a Simpsons caricature of Twilight Sparkle, underneath it.
In some scenes where the picture Comic Book Guy took of Bart and Milhouse for the "Banned for Life" section appears Milhouse's shirt is red.
Nelson has been said to be banned for life, yet he is in the line to see Tom Savini. Unless Comic Book Guy kicked him out, this isn't right. Also, in later episodes, Nelson is seen in the store. Though it is possible his banishment was lifted.
When Tom Savini told Comic Book Guy that he didn't swallow a cookie, Comic Book Guy's eyes briefly turn yellow.
Comic Book Guy accidentally pulled Tom Savani's hand off, and the hand crawls to the Comic Book Guy's pants. However, when Tom's hand gives Comic Book Guy a wedgie, Tom's missing hand is briefly restored.