The 'jackin' it San Diego' references are about Kony (2012) filmmaker Jason Russel. At the height of the film's popularity, a naked Russell was detained by San Diego PD for psychiatric evaluation after he vandalized cars and made sexual gestures.
The character of Bucky Bailey, the anti-bullying counselor, is drawn to resemble Bob Keeshan as Captain Kangaroo.
This episode was mainly based on a lip dub by Cypress Ranch High School which showed the harm in bullying and brought the issue to light. If you watch the lip dub on YouTube (about 5 minutes long) and then watch this South Park episode, you will see many similarities in the layout of the school, the students' actions during the bullying song, and a sign or two that were copied from Cy Ranch's video. It was definitely a proud moment in our school's history when this episode came out.
The three singers in the "Jackin' it in San Diego" song are a parody of The Kingston Trio, a band from the late '50s who popularized folk-pop. One of the members, Nick Reynolds, was a native of San Diego.
Donna Dooby is said to actually be Ellen Burstyn, she just used pseudonym much like Mary Kay Bergman did to protect her title as Snow White when she replaced Adriana Castelotti, although no one really knows why Ellen would do such a thing.