An incomplete list of production codes used during Marvel Productions' run. I hope to get verification on the remaining codes in the future.
4000: Mini-series/movies
(Note: Where a mini-series was taken forward to a full series, the retroactive title has been used for clarity.)
4004 E.T The Extra Terrestrial
4005 - 4009 GI Joe: The MASS Device
4012 My Little Pony: Rescue At Midnight Castle
4013-4017 Gallavants (produced as Episodes 1-5)
4018 - 4022 GI Joe: The Revenge of Cobra
4023 - 4025 The Transformers: More Than Meets The Eye
4028 My Little Pony: Escape From Catrina
4034 The Transformers: The Movie
4035 - 4039 Robotix
4040: Robotix: The Movie
4041 - 4045 Jem: Truly Outrageous
4046: Jem The Movie
4018 - 4022 GI Joe: The Revenge of Cobra
4023 - 4025 The Transformers: More Than Meets The Eye
4028 My Little Pony: Escape From Catrina
4034 The Transformers: The Movie
4035 - 4039 Robotix
4040: Robotix: The Movie
4041 - 4045 Jem: Truly Outrageous
4046: Jem The Movie
4053: Defenders Of The Earth (specific production unknown)
4054: My Little Pony: The Movie
4055 The Glo Friends Save Christmas
4056 The Inhumanoids
4057 GI Joe: The Movie
4064 Pryde Of The X-Men
4054: My Little Pony: The Movie
4055 The Glo Friends Save Christmas
4056 The Inhumanoids
4057 GI Joe: The Movie
4064 Pryde Of The X-Men
4066 Fraggle Rock: The Spring That Almost Didn't Happen (unproduced prime-time special)
4067 The Monster Bed
4067 The Monster Bed
4069 Time Challengers
Main series:
1981
5000 Spider-man (Syndication)
6000 Spider-man And His Amazing Friends
1982
Main series:
1981
5000 Spider-man (Syndication)
6000 Spider-man And His Amazing Friends
1982
100 The Incredible Hulk
200 Pandamonium
300 Meatballs & Spaghetti
1983
400 Dungeons and Dragons
1984
500 Muppet Babies
600 GI Joe
700 Transformers
1985
800 The Young Astronauts
900 Defenders of the Earth
7000 Little Muppet Monsters
7000 Little Muppet Monsters
1986
5201 My Little Pony
5202 Potato Head Kids
5203 The Glo Friends
5204 Moondreamers
5205 Jem
5206 Inhumanoids
1987
6501 Fraggle Rock (Animated)
6510 Muppet Babies
6520 Little Clowns Of Happytown
6530 Little Wizards
6701 The Transformers: The Rebirth
1988
6511 Muppet Babies
6551 Robocop
6560 Dino-riders
1989
6570 Rude Dog And The Dweebs
1990
6513 Muppet Babies
6580 Attack Of The Killer Tomatoes
6580 Attack Of The Killer Tomatoes
6590 Kid N' Play
1991
6514 Muppet Babies
6581 Attack Of The Killer Tomatoes
6581 Attack Of The Killer Tomatoes
6610 Bucky O'Hare
6630 Space Cats
6630 Space Cats