The title is a pun acronym of C.E.O. (Chief executive officer).
Dr. Hibbert's former stripper name "Malcolm Sex" is a reference to 1960s Civil Rights activist Malcolm X.
Mr. Burns attempting to seal Homer into the catacombs is a reference to Edgar Allen Poe's The Cask of Amantillado.
In one scene Lenny and Carl fight using plutonium rods as lighsabers from Star Wars. Lenny says "I say the Phantom Menace sucks more!". Carl says "I say Attack of the Clones sucks more!". Their argument alluded to the controversial reception of the then-recent entries to the Prequel trilogy, The Phantom Menace and Attack of the Clones (at the time the episode aired, Revenge of the Sith had not premiered yet).
During the Itchy & Scratchy cartoon, Itchy is seen dressed like Fonzie from the sitcom "Happy Days". The Season 1 & 2 theme of said show is also played during this part.
When Homer eavesdropped on Mr. Burns, Smithers stated that Mr. Burns was in trouble due to the U.S. Government discovering evidence that he dumped nuclear waste under Lego Land, California.
In addition, one can catch a glimpse of Frank Grimes's portrait with a line crossed through it when Mr. Burns pulls down the chart showing the hierarchy of the staff. This is one of many references to the character's death from Homer's Enemy (1997).
When Mr. Burns returns from Morocco and Homer asks where Smithers is, Mr. Burns explains that he's doing an 80-year sentence at a Turkish Prison, and also wonders aloud why Smithers would be so ecstatic about being sentenced there. This was a reference to The Midnight Express, where the main character was arrested and put into a Turkish prison because he attempted to smuggle drugs. Likewise, Smithers being pointed out as being "oddly happy" to be taken refers to the main character, during his prison sentence, committing a homosexual relationship with another prisoner, a further hint to Smither's orientation.
During his time as CEO of the power plant, due to the long hours keeping him from his family, Homer laments that "Bart won't be ten years old forever" — a joke on the fact that Bart has been ten ever since the series started over 20 years ago, and likely will be for the rest of the run.
When Marge tries to act nonchalant about Homer going to Moe's, she mentions "Gabba Gabba Hey", a reference to the Ramones' catchphrase and lyric from their 1977 song "Pinhead."
In his continued use of archaic speech, Mr. Burns reacts to his firing requesting "Smithers, get this bedlamite an alienist". A bedlamite is a lunatic, and an alienist is a doctor treating the mentally ill.