In The Amy Virus, Daniel compares Cyan Beaut's new name to a Phish groupie: "Remember those girls who used to show up at their concerts dressed up like neon-colored mermaids, and they all had names like Koi Pond?"
In the Community episode "Economics of Marine Biology", Magnitude is shown trying to come up with a new catchphrase on a chalkboard. Among the phrases on that board are "Step into the freezer" (a reference to "Tweezer") and "Bag it, tag it" (a reference to "Reba"). "Cactus!", which is also bassist Mike Gordon's nickname, may or may not be a third intentional Phish reference on the board.
In the first episode of Moonbase 8, Rook admits to being a "Phish-head", even doing merch for the band.
Harris, the stoner animal control worker from Parks and Recreation is a Phish fan who is regularly seen wearing the band's shirts. In one episode, Tom refers to him as having seen 200 Phish concerts. The character was played by show writer Harris Wittels, a devoted fan of the band (who saw them at least 300 times in his lifetime) who also hosted his own podcast on the band called Analyze Phish.
In "Lisa the Tree Hugger" Jesse warns his environmentalist friends that they cannot leave the tree "Not for a Phish concert, not even for Burning Man." Funnily enough, when the episode aired in November 2000, Phish had just entered a two-year hiatus from concert performances that they would not end until December 2002.
All four members appear in and voice themselves in "Weekend at Burnsie's", performing "Run Like an Antelope" at Homer's marijuana rally.
The jam band seen performing in the South Park episode "Die, Hippie, Die" resemble the four members of Phish, right down to being lead by a red-headed man with eyeglasses and a full beard a la Trey Anastasio.
.