He appeared in "I Never Met the Dead Man" when Peter Griffin decides that television is evil. Griffin says he has been watching it in his cell all day long. In the ensuing cutaway, Manson says that if he hasn't seen it then it's new to him.
Peter talks about his California family in "Brian Does Hollywood", a cutaway shows him asking Charles Manson and his followers not to embarrass him at a party in the Hollywood Hills.
A non-animated headshot of Manson appears in "Road to the North Pole" as one of the voices in Meg Griffin's head during the musical number "All I Really Want For Christmas".
In "Foreign Affairs", a stoned Peter confides with a stoned Chris that they should go on a killing spree in the Hollywood Hills, a reference to Charles Manson and his followers killing of actress Sharon Tate and 6 others over a 2 day period in 1969.
Stewie Griffin mentions Charles Manson as having a twisted childhood while preparing to torture The Simpsons' Nelson Muntz in "The Simpsons Guy".