Johnny O. Binome's joke in binary translates to "take my wife please".
There is a cameo from Sal and Harv, the workers from the Dire Straits music video "Money For Nothing," which was made by ReBoot creators Ian Pearson and Gavin Blair. The Dire Cell also gets their name from the band and plays part of one of the rhythms from the song.
The makers of the show were having difficulties with strict guidelines from the Board of Standards and Practices on what they could and couldn't show. They wouldn't allow anything too violent or suggestive. To poke fun at this, they included Emma, who shot down every act auditioning for one reason or another. The only one she accepted was the Village People parody, with the song "BS&P", presumably standing for "Board of Standards 'n' Practices". Hence, the lyrics "It's fun to play in a non-violent way". The "Program Sensor", Emma See, was specifically based on a particularly difficult BS&P official named Mary. She was reportedly not happy to find out she was parodied as this character.
When Megabyte first appears on stage, he emerges from a metal coffin. This is a parody of Iron Maiden, where during their 1990-1991 'No Prayer from the Road' tour, their cover-album mascot "Eddie" emerged from a coffin.
Hack and Slash's rotating drum set is a reference to Mötley Crüe drummer, Tommy Lee, who has used a rotating drum set during live shows.