I generally like to put the series in their own seperate continuites:
1. Original/Scrappy Doo Timeline
Everything from Scooby Doo: Where Are You through 13 Ghosts of Scooby Doo, plus the three tv movies from the 80's.
2. Pup/What's New Timeline
A Pup Named Scooby Doo, Scooby Doo Where Are You, and What's New Scooby Doo{and possibly Get A Clue also}. The events of SD: Where Are You take place in this timeline, except in the late 90's instead of the 60's.
3. Zombie Island Timeline
Everything from SD: Where Are You to the Scooby Doo Shou, plus all the DTV movies from 1998 to present.
4. Live Action Movie Timeline
Everything through the Scooby and Scrappy Doo, plus the two live action movies.
5. Mystery Begins Timeline
This is a new timeline since it's a orgin story and it takes place in 2009.
Scooby Goes Hollywood and Laff-A-Lympics are not in continuity. "Mystery Incorporated" would go directly after SD:WAY.
1. Original/Scrappy Doo Timeline
Everything from Scooby Doo: Where Are You through 13 Ghosts of Scooby Doo, plus the three tv movies from the 80's.
2. Pup/What's New Timeline
A Pup Named Scooby Doo, Scooby Doo Where Are You, and What's New Scooby Doo{and possibly Get A Clue also}. The events of SD: Where Are You take place in this timeline, except in the late 90's instead of the 60's.
3. Zombie Island Timeline
Everything from SD: Where Are You to the Scooby Doo Shou, plus all the DTV movies from 1998 to present.
4. Live Action Movie Timeline
Everything through the Scooby and Scrappy Doo, plus the two live action movies.
5. Mystery Begins Timeline
This is a new timeline since it's a orgin story and it takes place in 2009.
Scooby Goes Hollywood and Laff-A-Lympics are not in continuity. "Mystery Incorporated" would go directly after SD:WAY.