According to the DVD commentary, this episode has two directors due to the fact that Mark Kirkland (the original episode director) was going through a divorce at the time and hired Matthew Nastuk to take over.
Yo La Tengo performs a psychedelic rendition of the theme song over the end credits.
According to this episode, Seymour Skinner had been principal of Springfield Elementary for fifteen years, even though "The Principal and the Pauper" showed that he worked there for twenty years. D'oh-in' in the Wind likely took place five years before The Principal and the Pauper.
It is implied in this episode that Abraham Simpson forced Homer to be drafted into the Vietnam War due to embarrassment at the latter's insistence of wanting to be a hippie.
The end title for Mr. Burns' promo for the Nuclear Power Plant reads, "An Alan Smithee Film". From 1968 until 1999, this was a pseudonym used by directors who wanted to dissociate themselves from a movie that they felt was ruined due to loss of creative control or realizing that their project is a complete and utter failure.
Bartles & Jaymes, the wine cooler and malt beverage line; specifically, the men portraying Bartles and Jaymes in the product line's ads. The admen do have some similarities with Seth and Munchie, and both duos produce and sell beverages.
Ben and Jerry of Ben & Jerry's ice cream. This is the more likely possibility because Seth and Munchie have more in common with Ben and Jerry than they do with Bartles and Jaymes. Also, Ben & Jerry's most popular flavor is Cherry Garcia, which was named for Grateful Dead founder and frontman Jerry Garcia, and the episode contains some Dead references.
When Homer tries to get Marge to go braless, saying "Free the Springfield Two," it is a reference to the 1960s protest slogan "Free the Chicago Seven".
Some things in the freak-out and after—such as Homer becoming "The Cosmic Fool", the psychedelic paint job on the car, and the juice being spiked with drugs are loosely based on the antics of the Merry Pranksters.
Homer refers to the "doors of perception" during the freak-out - this is Aldous Huxley's 1954 book where The Doors got their band name.
Barney Gumble sees a three-eyed monster, which frightens him. He then throws down the bottle of juice and quickly drinks some Duff Beer in order to overcome it. A pink elephant marches through the door to Barney's aid and stomps on the monster. The elephant resembles one seen in the Disney animated film "Dumbo" when Dumbo mistakenly becomes drunk.
Ned Flanders is driving and sees the Grateful Dead Dancing Bears, Melody and Verse, and the Skeleton, also from the Grateful Dead, who says "Mornin' Ned." They are followed by the Marching Hammers from Pink Floyd's The Wall marching across the street and the Rolling Stones' "Lips and Tongue". Series creator Matt Groening has admitted to being a huge Dead, Floyd and Stones fan.