Despite the heavily implied Fraphne (Fred/Daphne) relationship throughout the franchise, the pairing has only been officially confirmed in nine episodes and movies over the span of 50 years.
Scooby-Doo and the Witch's Ghost (not officially confirmed, but very heavily implied at one point)
Scooby-Doo! Stage Fright
Scooby-Doo! Mecha Mutt Menace
Scooby-Doo & KISS: Rock and Roll Mystery
Scooby-Doo 2: Monsters Unleashed
Scooby-Doo 4: Curse of the Lake Monster
Scooby-Doo! Mystery Incorporated