There have been many explicit references to other bands on The Simpsons, including Sonic Youth, Smashing Pumpkins, Peter Frampton, Michael Jackson, Cypress Hill, Steve Miller Band, Bob Marley, The Ramones, Red Hot Chilli Peppers, Spinal Tap, Pink Floyd, Grand Funk Railroad (Homer's favorite band), and the Beatles.
So, for many years, fans sought references to Phish on the show, sometimes stretching reason. Bart has called Willie and Millhouse Lawnboy, but that's not a Phish reference; it's a brand of mower. Homer danced to "Baby Elelphant Walk", Otto whistled "Frankenstein", and Principal Skinner sang "Ragtime Gal", all of which Phish has played - but none of which is a Phish original. In one episode ("Besharps"), Moe's Tavern is renamed Moe's Cavern and Revolution #9 is performed; those are (also?) both Beatles references, though in the same episode there's an "Antelope crossing" sign as Wiggam pulls Homer over. In other episodes, Homer bootlegged bathtub gin (a common practice during prohibition), Bart joked about changing a "fishbulb" while Homer stoood on a box of Mr. Sparkle detergent, Homer told Barney "I could punch you in the nose", Lisa had an evil twin named Eliza, and Jaspar and Lisa have both stepped into freezers. Such instances were suggested by fans as thinly veiled nods to the band - though also ridiculed by others as wishful thinking.
Then came the Phish episode, including all four band members in a Springfield benefit concert.
To note, Phish has teased the theme to The Simpsons as part of its "secret language" - though last played it 12/3/97.
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