Shaggy & Scooby-Doo Get a Clue! was broadcast over the WB network in 2006. Its animation style was radically different from previous Scooby-Doo series. Eric Radomski produced this series, and Joseph Barbera and Sander Schwartz were the executive producers. It was the last animated series that Joseph Barbera was involved in before his death in December 2006.
In this series, Scooby and Shaggy live in the opulent mansion of Shaggy's Uncle Albert Shaggleford. They have a transforming Mystery Machine, similar to the Chan Van in The Amazing Chan and the Chan Clan, and special top-secret Scooby Snacks infused with nanomachines. These biscuits enable Scooby to change his physical form as the situation requires.
The new Scooby Snacks are coveted by a gang of master villains led by Dr. Phineus Phibes, so Shaggy and Scooby have to keep the snacks out of criminal hands while solving mysteries.
- Jeff Bennett as Dr. Phineus Phibes, Agent 2 and Ricky
- Casey Kasem as Dr. Albert Shaggleford
- Scott Menville as Shaggy Rogers, Agent 4 and Dr. Trebla
- Jim Meskimen as Robi, Agent 1 and Mark
- Frank Welker as Scooby-Doo, Agent 3, Agent 13 and Menace
- Shags to Riches
- More Fondue for Scooby-Doo
- High Society Scooby
- Party Arty
- Smart House
- Lightning Strikes Twice
- Don't Feed the Animals
- Mystery of the Missing Mystery Solvers
- Chefs of Steel
- Almost Ghosts
- Pole to Pole
- Big Trouble
- Operation Dog and Hippy Boy
- Shaggy and Scooby World
- Almost Purr-fect
- Inside Job
- The Many Faces of Evil
- Cruisin' for a Bruisin'
- There's a Doctor in the House
- Super Scary Movie Night
- Runaway Robi
- Don't Get a Big Head
- Scooby Dudes
- Zoinks the Wonderdog
- Uncle Albert Alert
- Fred Jones, Daphne Blake and Velma Dinkley were not regular characters in this series, though they did make rare but brief appearances, and sometimes cameos.
- This is the first Scooby-Doo series to center around Shaggy and Scooby-Doo since The Scooby and Scrappy-Doo/Puppy Hour in 1982.