The title of this episode is a reference to the expression "The birds and the bees", used by parents when explaining a sexual relationship to a child.
Music from the episode:
"Deck the Halls" (Lisa plays this on her saxophone as she walks out of the class)
"Amazing Grace" (Groundskeeper Willie plays it on his bagpipes while mourning for the deceased bees)
"Hip Hop Hooray" by Naughty By Nature (played during the gorilla mascot scene)
"Sea of Love" by The Honeydrippers (when the queen bee is being introduced to the Africanized bees)
"Call to the Cows" by Rossini (when the bees are released in the old greenhouse)
Since the intro is done in a Christmas theme, Mr. Burns appears as Ebenezer Scrooge and Smithers appears as Jacob Marley.
The bee tombstone that set Jerry Seinfeld a reference to the 2007 DreamWorks film Bee Movie where Seinfeld played as the voice of Barry.
In Homer's fantasy about a future without honey, the robot that offers him some artificial honey and then compresses him into a cube resembles WALL-E from the Disney/Pixar film of the same name.
The original home of the Springfield Celtics/Excitement, the Springfield Sports Palace, is very similar in appearance to the former home of the Boston Celtics and Bruins, Boston Garden. That arena was demolished in 1998 after being replaced by TD Garden.