Shout Out: Richard the raccoon might be a nod to a kids' magazine entitled Ranger Rick, whose mascot was also a raccoon.
There's one early strip◊ where Amy has a nightmare that Timmy is an evil genius. She wakes up Tom and informs him that they are never watching Family Guy again. (The show isn't mentioned by name, and Tom wonders if Amy means The Venture Bros..)
Sabrina: "What comes to mind when you hear 'Sabrina?'" Amy: "Other than 'Teenage Witch?'"
When you consider that Sabrina's mother Endora and sister Tabitha share names with characters from Bewitched, this may qualify as Theme Naming as well.
Zig also◊ pulls a Zii on one of her detractors. It's even titled "Menage a what?". However, unlike the base breaking actions of Zii, this one is with an already divorced single mother, and not the cause of said divorce.