Here are the ones with made-up episodes:
Gordon Runs away and other stories:
Gordon Runs Away
Emily`s 2nd adventure
Henry,James and the flood
Oliver gets it right
The NEW Grand Opening
Duncan takes charge
SONG: Hail to Rusty

Helping Out:
Emily To The Rescue
Terence`s New Field
Toby`s Replacement Coaches
Harold,Edward & The Soccer Field
Duke & Duchess
Mavis At The Docks
SONG: Rock N Roll With Duncan

Fun on Sodor!:
Thomas` Ice cream surprise
James And the castle
Toby And Bertram`s Great Race
Spencer & Oliver
Edward,Henry And Mavis
Toad

Bill,Ben And Oliver & Other Stories:
Bill,Ben & Oliver
Duck`s Big Mistake
James Saves The Day
Percy & The Chocolate Factory
Gordon And The Cows
Thomas helps Murdock
Molly And Mavis
Rusty`s Big Adventure
SONG: The Molly Song

Engine Adventures!:
Thomas And The New Snowplough
Smudger`s Holiday
James,Toby And The Carnival
Donald`s Clock Tower
Duncan And Duke
A Bad Day For Gordon

Halloween!:
Percy`s Ghostly Route
Duncan meets a Ghost
Molly And The Haunted House
Sir Handel And The Curse
Diesel`s Big Scare
Runaway Percy
SONG: Scaredy Engines

James Saves The Day & Other Stories:
James Saves The Day
The Runaway Coaches
The Queen Returns
Rusty,Duncan And The Golden Coach
James And The Trouble With Leaves
Edward`s Special Special
SONG: Happy Engines

And here are the ones with real Episodes:
Best Of Peter Sam:
Peter Sam & The Refreshment Lady
Trucks!
You Can`t Win!
Special Funnel
The Refreshment Lady`s Stand
The Magic Lamp
SONG: Little Engines

Best Of Duncan:
Home At Last
Rock N Roll
Passengers & Polish
Duncan Gets Spooked
Dunkin` Duncan
Faulty Whistles
The Runaway Elephant
Duncan And THe Old Mine
SONG: Come For The Ride

Best Of Bill & Ben:
The Diseasel
One Good Turn
Heroes
Double Teething Troubles
Salty`s Secret
Buffer Bother
Bill,Ben & Fergus
SONG: Every Cloud Has A Silver Lining

The Best Of Donald & Douglas:
Brake Van
The Deputation
Donald`s Duck
Thomas & The Missing Christmas Tree
Escape!
Twin Trouble
Bad Day At Castle Loch
SONG: Donald`s Duck

Bad Day At Castle Loch & Other Stories:
Bad Day Castle Loch
Snow Engine
The Runaway Elephant
Fegus Breaks The Rules
No Sleep For Cranky
Gordon Takes A Tumble

Best Of Duck:
Duck Takes Charge
Pop Goes The Diesel
Dirty Work
A Close Shave
Bulgy
All At Sea
Fish(1)

Best Of James 2:
Foolish Freight Cars(Carlin)
Make Someone Happy(Brandon)
James And The Trouble With Trees(Brandon)
James And The Red Balloon(Brandon)
James And The Queen Of Sodor(Brandon)
James Goes Too Far(Brandon)
James Gets A New Coat(Brandon)
Keeping Up With James(Brandon)
SONG: James The Really Splendid Engine

The Best Of The Diesels:
The Disesal
Daisy
Percy`s Perdicament
Pop Goes The Diesel
Mavis
Toby`s Tightrope
Rock N Roll
Rusty To The Rescue
Diesel Does It Again
Middle Engine
No Sleep For Cranky
Salty`s Secret
Trusty Rusty
Tuneful Toots
Thomas` Day Off
SONG: Down By The Docks

The Best Of Seasons1-9:
Thomas And Bertie
Duck Takes Charge
The Trouble With Mud
Paint Pots And Queens
Cranky Bugs
A Bad Day For Harold The Helicopter
Gordon & Spencer
Henry & The Wishing Tree
Duncan And The Old Mine
SONGS:
Thomas` Anthem
Engine Roll Call