During The Beat A Dead Horse Tour, Primus is not performing a static setlist; they are playing a different setlist each night, with only about 2 or 3 songs being consistently played in each set. In a surprising move, Primus performed "Wynona's Big Brown Beaver" quite often on this tour — the first time they have done so in 7 years, which was in Houston Texas. "Shake Hands With Beef" has also been played this tour a few times, for the first time ever with drummer Tim Alexander In Ft. Worth Texas. Another notable performance was when Claypool was sick during the Philadelphia show, and his voice wasn't in top condition. This led to them playing the rare "Hamburger Train" and giving drummer Tim Alexander a chance to flex off his drumming skills while Claypool chimed in with his Whamola, then during "Too Many Puppies" they performed the first "Master of Puppets" tease since 1995.
While playing the song "American Life" at the Roseland (New York) show, the metal barrier became unhinged from moshing, which prompted the band to stop playing for 15 minutes while the barrier was getting fixed.
On November 12, 2006 at the Orpheum Theater in Boston, Les Claypool bantered with a fan named Gus after Claypool's microphone temporarily malfunctioned. Gus shouted for guitarist Larry LaLonde to sing the entire rest of the set. Claypool then asked the fan's name and upon hearing it said "Gus? Is that really your name?" Then, Claypool asked Larry to sing the entire rest of the set, stopping the song and counting off. Larry then replied in an awkward sing-song, "The entire rest of the set!" which was received with loud cheering and laughter.
Unusual for a Primus tour, the concert staple Tommy the Cat was played only once in San Diego during this tour.