Kidnapping Daphne Blake

A long-running theme of having the various incarnations of Daphne Blake getting kidnapped or captured by the antagonist.

Scooby-Doo, Where Are You!

 * Decoy for a Dognapper: Kidnapped and tied to a post by the Ghost of Geronimo.
 * A Gaggle of Galloping Ghosts: Chased by Frankenstein into a dungeon.
 * Which Witch is Which?: Kidnapped and bound and gagged by the Witch and the Zombie.
 * Go Away Ghost Ship: Kidnapped and chained up by Redbeard's Ghost along with Fred and Velma.
 * Mystery Mask Mix-Up: Kidnapped and bound and gagged by the Scare Pair.

Dynomutt, Dog Wonder

 * The Wizard of Ooze: Trapped in a net high in a tree with the others, with alligators below and a beaver gnawing on the tree to make it a deathtrap.

The New Scooby-Doo Movies

 * Sandy Duncan's Jekyll and Hyde:
 * The Haunted Candy Factory:

The Scooby-Doo Show

 * A Frightened Hound Meets Demons Underground:
 * The Creepy Creature of Vulture's Claw:
 * A Menace in Venice:

The New Scooby and Scrappy Doo Show

 * Scooby the Barbarian:
 * Scooby of the Jungle
 * Scoobsie: The Phantom of the Soaps tried to kidnap Daphne, but she was rescued by Scrappy-Doo.
 * The Scooby Coupe:

The New Scooby-Doo Mysteries

 * Ghosts of the Ancient Astronauts: Held prisoner in a zombie village.

The 13 Ghosts of Scooby-Doo

 * Scoobra Kadoobra:
 * It's A Wonderful Scoob: Tied up by Time Slime, his slave in an alternate future.

A Pup Named Scooby-Doo

 * Wanted Cheddar Alive:
 * The Computer Walks Among Us:

What's New, Scooby-Doo?

 * Big Scare in the Big Easy:
 * High-Tech House of Horrors:
 * New Mexico, Old Monster:
 * E-Scream: The Osomons capture a virtual Daphne in a box.

Scooby-Doo! Mystery Incorporated

 * Revenge Of The Man Crab:
 * In Fear Of The Phantom:
 * Escape From Mystery Manor:
 * The Siren's Song:

Batman: The Brave and the Bold

 * Bat-Mite Presents: Batman's Strangest Cases!:

Animated films

 * Zombie Island: Restrained by the magic of a voodoo doll.
 * The Monster of Mexico:
 * The Loch Ness Monster:
 * Pirates Ahoy!
 * The Samurai Sword:
 * Music of the Vampire:

Live-action films

 * Scooby-Doo:

Novels

 * Scooby-Doo! and the Zombie's Treasure:
 * Scooby-Doo! and the Farmyard Fright:
 * Scooby-Doo! and the Deep Sea Diver:

Comics

 * Scooby in the Booby Hatch!: Put in an asylum by her Aunt Mildred.
 * Revenge, Inc.: Trapped in her own mind by a hypnotic ray.
 * Scooby-Doo in The Dragon's Eye Conclusion: Just Deserts: The whole gang was tied up by the villain.

Deleted scenes

 * Scooby-Doo's unused opening: