There are a total of 50 clues in this game. Each area with a point and click Scooby and Shaggy Section contains clues except for the area which contains the entrance to the Faux Ghost.

All Clues Picture Guide: https://imgur.com/a/5gubCCM

Mystery Inc. Area 1: 2 Clues

Coolsonian Museum Area 1: 4 Clues Area 2: 4 Clues

Wickles Manor Area 1: 4 Clues Area 2: 5 Clues

Faux Ghost Area 1: 4 Clues Area 2: 3 Clues Area 3: 3 Clues

Old Tyme Mining Town Area 1: 3 Clues Area 2: 6 Clues Area 3: 3 Clues

Lab Area 1: 3 Clues Area 2: 3 Clues Area 3: 3 Clues