Yes.

Additionally, more than a few Simpsons episodes contain loose or possible references to Phish, such as

• Homer bootlegging "bathtub gin" or saying, "Barney, I could punch you in the nose";
• various appearances of Edgar Winter's "Frankenstein" (including Otto whistling it, Homer going back in time and hearing it, and someone listening to it on headphones) which Phish covers,
• Millhouse being called "lawnboy" by Bart.
• While Homer stood on a box of Mr. Sparkle detergent, Bart joked about changing a "fishbulb".
• At the FBI headquarters in the X-Files episode, there's a picture of J. Edgar Hoover on the wall in something akin to Henrietta's dress, though it was purple with yellow flowers not purple with orange loops.
• Several characters (including Jaspar and Lisa) have prominently stepped into a freezer (referencing "Tweezer")
• Bart calls Willie "Lawnboy" when (in the Tree house of Terror VI episode) he turns into a mower, although there are Lawnboy brand mowers.
• Principal Skinner sings "Ragtime Gal" over the school P.A. system when Bart gains magical powers (which he also used to turn Homer into a jack-in-the-box)
• In one episode ("Besharps") alone, there's an "Antelope Crossing" sign when Wiggam pulls Homer over, Moe's Tavern is renamed Moe's Cavern, and inside a wild performance of "Revolution #9" is performed.
• In the dancing Homer episode, Homer danced to "Baby Elephant Walk", which Phish performed to end The Lemonwheel.
• In one episode, Lisa's evil twin was named Eliza (also the name of Trey's eldest daughter).

Simpsons episodes have made explicit references to other bands: 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.

Phish last played the Simpsons theme on 12/3/97.

Thanks also to John Keller, Dirtboy, Thomas and KJ, Mike D. Kraft, Chuck Doyle, Russ Barnett, Paul Levy, Michael Vickers, Jason Weiss, Gareth Hughes, John Seitz, Elliott @ Purdue, Yangety, Richard Slater, and Nickthe7.