I am gonna have factor in several things: Subjective opinions (A lot of personal opinions), Objective opinions (as in what I think do the best job without factoring in any kind of bias), the iconic factor, and how well the represent their respective series. There's gonna be a lot lol
SDWAY: (And I won't just allow myself to say all of them lol)
What a Night for a Knight
Hassle in the Castle
A Clue For Scooby Doo
What the Hex Going On
The Backstage Rage
Bedlam in the Bigtop
A Gaggle of Galloping Ghosts
Which Witch is Which
Go Away Ghost Ship
Spooky Space Kook
A Night of Fright is No Delight
Nowhere to Hyde
Jeepers It's the Creeper
Haunted House Hang Up
NSDM:
Dynamic Scooby Doo Affair
The Frickert Fracas
Guess Who's Knott Coming to Dinner
The Secret of Shark Island
Ghost of Bigfoot
The Caped Crusader Caper
The Loch Ness Mess
TSDS:
High Rise Hair Raiser
Watt a Shocking Ghost
Headless Horseman of Halloween
Harum Scarum Sanitarium
No Faced Zombie Chase Case
Ghost of the Bad Humor Man
Vampire Bats and Scaredy Cats
Chiller Diller Movie Thriller
Spooky Case of the Grand Prix Race
Creepy Cruise
To Switch a Witch
Scrappy era:
The Scarab Lives
I Left My Neck in San Francisco
A Fit Night Out For Bats (something has to represents the shorts, and this is the best choice lol)
Wedding Bell Boos
Happy Birthday Scooby Doo
A Halloween Hassle at Dracula's Castle
A Nutcracker Scoob
That's Monstertainment
APNSD:
A Bicycle Built for Boo
Wanted Cheddar Alive
The Schnook That Took My Comic Book
Snow Place Like Home
Chickenstein Lives (Perfectly encapsulates this series)
Were Doo of Doo Manor
WNSD:
There's No Creature Like Snow Creature
Big Scare in the Big Easy
Lights Camera Mayhem
Mummy Scares Best
Simple Plan and the Invisible Madman
A Scooby Doo Halloween
Fright House of a Lighthouse
Farmed and Dangerous
A Scooby Doo Valentine
E Scream
Get a Clue:
Sorry, I got nothing for this one. Perhaps Doo or someone else who knows more about this series (or actually likes it) would have more insight here
SDMI:
Beware the Beast From Below
Mystery Solvers Club State Finals
All Fear the Freak
Night Terrors
Wrath of Krampus
Nightmare in Red
Man in the Mirror
Come Undone
Be Cool:
Party Like its 1899
Some Fred Time
In Space
Doo not Disturb
Guess Who:
Haunt of a Thousand Voices