Crybaby Clown also seems like an allusion to Hamill's role as Macendale/Hobgoblin on Spider-Man: The Animated Series, since the villain is more practical-minded than Joker, and both are shallow pretty-boys who romance the local rich girl who is fed up with her distracted ex/potential beau and turn to destructive crime waves in the name of money/fame. Both Daphne and Felicia Hardy are made to feel like fools when their date is unmasked.
Early on in season two, Velma seems to have become pretty good friends with Hot Dog Water. It probably doesn't hurt Hot Dog Water's voice actress Linda Cardellini has a bit of a past relationshipwith Velma...
In Episode 12, Harlan Ellison spouts out a paragraph about the monster, full of "f" words (but not theF Word).
Tim Matheson is basically voicing an adult version of Jonny Quest, to the point where the character in season two is radically redesigned from his teenager self to resemble Jonny.
Doing It for the Art: The reason Baylor Hotner initially became Crybaby Clown, to do research for his next film.
Fandom Nod: In "Dance Of The Undead", when asked why the Hex Girls went back to their original outfits (resembling the ones worn in Witch's Ghost), they say that fans just preferred their original look. Some fans complained about their new look, so this is more than likely a little in-joke.
Fan Nickname: The Nibiru Entity is actually referred to as The Evil Entity in the series proper.
Matthew Lillard, who's played Shaggy before, now provides the voice of Shaggy after the original voice actor for him (Casey Kasem) retired from doing his voice after 40 years of loyal service, though Kasem is still on the show, only now as Shaggy's father.
Speaking of parentage, Brad Chiles, Fred's real father, is voiced by Tim Matheson, the original Jonny Quest.
Fred Jones Sr. is often referred to as Mayor Jones.
Scooby-Doo meets Scooby the seal.
Non-Singing Voice: Averted with the Hex Girls and Daphne. All of the actresses performed the songs played within the show.
Screwed by the Network: The first season was split in half and aired over two years. The second season was announced to premiere in May 2012, but the episode was not aired. After it didn't air it was announced that the episode would air on July 10 (almost a full year after the previous episode), but again didn't air. New episodes finally started on July 30, over a full year after the first season ended, and were burned off at 2PM monday-friday for a few weeks and briefly mis-labeled as Tom and Jerry Tales.