When Harry Goz, who voiced Captain Murphy, died in 2003, the first episode produced after his death introduced Tornado Shanks, a new regular character voiced by Harry's son, Michael Goz.
In "Murphy Murph and the Feng Shui Bunch" there are two scenes that has a telephone with graffiti on and around it. The second scene you see the phone there is some graffiti that says "This graffiti is not different stop pausing".
Two episodes ("Dearly Beloved Seed" and "Butchslap") are credited as being written by "mcheshpants420". He was apparently a fan who frequented the message boards on the shows official site with the user name "mcheshpants420." Supposedly, the producers actually accepted his script ideas. It was later uncovered that meheshpants420 was actually Chris Ward aka MC Chris, who voiced Hesh and contributed to the show regularly. It was all part of an elaborate joke.
The Bebop cola machine has the following sodas (all of which are puns on famous jazz musicians): Root Bird, Gilberto Grape, Artie Shawberry, Kiwi Holliday, Peachmo, John Cola-Trane, Don Wild Cherry, Vince Guavaldi, Dave Bruberry, Cab Colaway, Dexterade, Nina Lemone, Mango Reinhardt, Getzberry, Fizzy Gillespie, Marian McPineapple, Or'ngette Coleman, Mingus Dew, Plain, Diet Plain.
One of the many pieces of graffiti around the phones ("My backpack's got jets") is actually a line from the song "Fett's Vette" by Chris Ward (who provides the voice for Hesh).