Before I can guide you to the scrumptious IPs at your disposal for custom decks, I need to clarify what this is.

This is NOT me granting you anything. I hold no power over any of these IPs. I am by no means associated with the companies listed. I am by no means held accountable if a company changes their mind or otherwise revokes your license.

What this IS is a guide and list to IPs whose owners have given the greenlight on fan creations to the point you can safely upload the otherwise copyrighted content onto Steam Workshop without SotM moderators needing to raise an eyebrow.

Bear in mind that most IP holders come with fancy guidelines and requirements regarding the usage, and I will list these requirements for your convenience.

Greater Than Games and Handelabra Games, bless their souls, are quite strict on the rules. And why wouldn't they? Lawyers cost a lot, so better be safe than sorry. This too comes with strict enforcement of Steam's own Workshop rules, which you have to agree on before uploading anything.

In section 2. D. it clearly states that third-party properties require some form of permission to be used by you. Now, most companies are tight-lipped. Any and all fan art of some are technically illegal. They allow it anyways because, hey, free advertising. But failure to enforce their IPs can lead to the rights of the property to be revoked. The answer: a legal policy or declaration handing people the right to create fan art. If the fan art is not specified or it mentions interactive works as allowed, you can upload custom decks featuring their properties here, since you now have a "license" of sort.

Despite the legalities below and above, there is something that should be common etiquette.

Provide proof.

For your sake every column about a company whose IPs are allowed to be used have a link to the source documents. They detail even more than what I discuss here, things that mostly discuss the legal jargon and covers the basics. So do keep in mind to copy those links and put them on your Workshop pages when applicable, as they can act as proof when moderators check your upload.

Do it immediately.
It saves you time, it saves the moderators time. Those long forms proves everything I state in this guide, as of 14.10.2023

Greater Than Games and Handelabra Games do not allow content based on the game's universe. It is strictly stated that, by no means, may you implement artwork from the game itself or recreate characters.

You are encouraged to feature established characters in your card art alongside your own character.
You cannot pick a background character and make them a deck.
You cannot create a new hero or villain based on the Sentinels property.

What you CAN do, is create a brand new variant of an existing character, as long as it follows original ideas. You cannot use concepts that already exist within the intellectual property.

Legal document:
https://docs.google.com/document/d/e/2PACX-1vSWcmz_Popqw1w7rS-Nq0WxGPkt_JFF1SSUCOojz_t2A94lD6tYs15P_c2h09NIRrrhmo4ElKz3NhfS/pub

All companies beneath this section let you use their copyrighted IPs. Sometimes there are restrictions and rules that follow, and it is best to honour such demands.

Bear in mind that all companies below hold the right to revoke the license that lets you use their IPs in fan creations. Do not dishonour or hurt their brands.

In the Steam Workshop Legal Agreement, section 2. D., Valve grants you the full legal right to use their IPs on the Workshop. This means literally everything they own, and with minimal restrictions.

With this policy you are entirely allowed to create and upload Workshop content based on the following franchises:

Team Fortress
Portal
Half-Life
Left 4 Dead
Dota
Counter-Strike
Day of Defeat
Ricochet
Alien Swarm

There aren't any specific restrictions or demands of what you have to do. Simply create and upload. Just don't monetize it in any way.

Legal document:
https://store.steampowered.com/subscriber_agreement/

Microsoft has an entire page dedicated to giving you limited rights to all their owned properties. That's right: all of it. Everything from 343 to Rare, it's yours to play with provided that you follow the guidelines.

First things first, don't use official logos.
Don't make indecent things with it.
Don't make it seem official.
And always put this disclaimer on your Workshop page:

[Name of the Microsoft Game] © Microsoft Corporation. [The title of your Item] was created under Microsoft's "Game Content Usage Rules" using assets from [Name of the Microsoft Game], and it is not endorsed by or affiliated with Microsoft.

You also need to link to the rules, which I have below.
Legal document:
https://www.xbox.com/en-us/developers/rules

Following these rules, you have the right to use:

Halo
DOOM
Elder Scrolls
Fallout
Prey
Banjo-Kazooie
Sea of Thieves
Conker's Bad Fur Day
Kameo: Elements of Power
Viva Piñata
Hi-Fi Rush
Whacked!
Costume Quest
Psychonauts
JetPac
Perfect Dark
Killer Instinct
Battletoads
Blast Corps
Jet Force Gemini
Starfield
Microsoft Flight Simulator
Grabbed by the Ghoulies
Gears of War
Brutal Legend
We Happy Few
Fable
Skylanders
Overwatch
World of Warcraft
Starcraft
Crash Bandicoot
Spyro the Dragon
Call of Duty

And more that I have failed to remember. Basically, if Microsoft's companies own it you can use it.

Minecraft was left out of Microsoft's guidelines. I don't know why, but surely some form of agreement was made.

Good news is: Mojang is even more relaxed on fan creations! Create whatever your heart desires when it comes to Minecraft-related creations. Just remember to:

Make it clear you're not affiliated with Mojang.
Do not use game assets.
Do not put Minecraft as the first word in your Workshop name.

Other than that you are ready to go. No unlawful or distasteful content, obviously.

Legal document:
https://www.minecraft.net/en-us/terms#terms-brand_guidelines

The creators of Bendy and the Ink Machine have gracefully given you their permission to make fan content. You may use their IPs as long as you follow these rules:

Make it clear you are not affiliated with Joey Drew Studios.
Make it clear your fan creation is not official.
Don't use any branding or names as the first part or word in the title of the Workshop upload.
Example: "Bendy the Ink Creature" is NOT fine. "From the Ink: Bendy!" IS fine.
You must put this disclaimer on the Workshop page:

NOT AN OFFICIAL BENDY AND THE INK MACHINE PRODUCT. NOT APPROVED BY OR ASSOCIATED WITH JOEY DREW STUDIOS INC.

And with that, you're good to go! Custom decks are yours to design now. As always, be respectful and no distasteful usage.

Legal document:
https://www.joeydrewstudios.com/fancontent

Epic Games has a fancy fan creation policy that grants you the right to create using their IPs, provided that you do it respectfully. Their rules are as follow:

Do not imply the Workshop material is in any way official.
The fan creations must be appropriate for the original intended audience of the IP.
You must put the following disclaimer on your Workshop page:

Portions of the materials used are trademarks and/or copyrighted works of Epic Games, Inc. All rights reserved by Epic. This material is not official and is not endorsed by Epic.

Following these rules lets you use the following brands, and more that I may miss:

Fortnite
Jill of the Jungle
ZZT
Unreal Tournament
Jazz Jackrabbit
Xargon
Fall Guys
Rocket League
Undertow
Infinity Blade
Shadow Complex

Legal document:
https://www.epicgames.com/site/en-US/fan-art-policy

Paizo grants its community of fans the right to use and reference their lore, with a few restrictions.
You may use Pathfinder and Starfinder content as long as you abide by these rules:

Be respectful to Paizo and the IPs.
Do not imply you are affiliated with Paizo.
You MUST register and describe your fan project at: https://paizo.com/community/communityuse/registry
You must put the following disclaimer on your Workshop page:

[This website, product name, Twitch show title, etc.] uses trademarks and/or copyrights owned by Paizo Inc., used under Paizo's Community Use Policy (paizo.com/communityuse). We are expressly prohibited from charging you to use or access this content. [This website, product name, Twitch show title, etc.] is not published, endorsed, or specifically approved by Paizo. For more information about Paizo Inc. and Paizo products, visit paizo.com.

Successfully following the rules lets you create content based on Pathfinder and Starfinder. You may even use a select number of icons and art pieces, but alas I cannot and will not share them here.

Legal document:
https://paizo.com/community/communityuse

Square Enix has rather confusing and convoluted documents. But, in short, you do get access to their IPs. Just not their most popular works.

Square Enix is split between two different divisions, and only the west division has written a document. So not everything is covered, and they leave rules open to be specific on a per-game basis.

Follow these rules and you may use Square Enix (west)'s brands for fan creations:

Do not use Square Enix trademarks, like game titles and the company name, other than to describe what your creation is about.
You must make it loud and clear that your creation is not official.
You must be wary of spoilers in your creation, and if you have any you MUST make it clear.
You may not upload Square Enix fan content in the same Workshop upload with other brands.
You must include the following disclaimer on you Workshop page:

© Square Enix

Successfully following these rules lets you legally upload the following games:

Life Is Strange
Just Cause
Forspoken
Sleeping Dogs
Final Fantasy XVI
Heroes of Ruin

I may not remember nor know all of the brands, so some may have been missed. A reminder that Tomb Raider and Deus Ex were sold to Embracer Group, and therefore don't apply to this policy. Hitman's owner, IO Interactive, bought their own independence and therefore their brands don't apply either.

Reminder that this policy only applies to Final Fantasy XVI, no other entries in the Final Fantasy series.

Legal document:
https://www.square-enix-games.com/en_GB/documents/materialusagepolicy

For some reason Square Enix' eastern division has no fan content policies whatsoever (as far as I could find), except for the NieR series specifically. The document is purely in Japanese, so the use of Google Translate or other forms of translation is required. My tip is to access the site with your phone, and let it automatically translate the page for you.

To legally upload fan content of the NieR brand, follow these rules:

Do not use ripped game content, not even traced work.
Make it clear your work is not official and not affiliated with Square Enix.
Don't damage the brand in any way.

Once again, use a translator of some kind to read this exclusively Japanese document.
Legal document:
https://nierreincarnation.jp/fans_guideline.html

KONAMI has a very relaxed copyright policy. Literally just three paragraphs explaining you can use copyrighted content for anything as long as you don't spoil the plots. They reserve the right to smite down whatever they think is objectionable. So, while you do have permission, remember that KONAMI still demands respect to both themselves and their brands.

Due to the relaxed nature, I shall offer my own reminders of good etiquette:

Clearly display the fan content as unofficial.
Do not spoil the plots of the IPs.
Respect the brands.

If you follow good etiquette then KONAMI should have no issues with you creating fan content based on:

Metal Gear
Super Bomberman
Castlevania
Yu-Gi-Oh!
Zone of the Enders
Silent Hill
Frogger

Among many other brands I'm not aware of.

Legal document:
https://eu-support.konami.com/hc/en-gb/articles/9648771731479-Copyrights-Career-Opportunities-Goodies

Paradox famously loves mods and user generated content. That said, not everything they make is under their specific license. Everything that is in their power is free game, on a small amount of conditions. As always, use it with respect.

Do the following and everything should be a-ok:

Content shall not be unlawful or inappropriate.
It may not violate any contracts or common sense.
Content should be non-commercial.
Clarify you are not affiliated with Paradox.

If the content uses the World of Darkness brand, these rules apply as well:

Use one of the two Dark Pack logos on screenshots on the Workshop page and anywhere else when advertising it. The logos are provided below.
Post the following on the Workshop page and anywhere else you advertise:

"Portions of the materials are the copyrights and trademarks of Paradox Interactive AB, and are used with permission. All rights reserved. For more information please visit http://worldofdarkness.com."

If you do all of the above, you have permission to use the following brands:

World of Darkness
Magicka
Cities: Skylines
Stellaris
Crusader Kings
Age of Wonders
Prison Architect
Europa Universalis
Hearts of Iron

And any other Paradox owned IP I've forgotten.

Paradox mod policy:
https://legal.paradoxplaza.com/eula

World of Darkness Dark Pack:
https://www.worldofdarkness.com/dark-pack

Dark Pack logos with and without red border:
With red border.[s3-eu-north-1.amazonaws.com]
Without red border.[s3-eu-north-1.amazonaws.com]

All games following this column are allowed in a big ol' MAYBE sign.
They have conflicting messages in some form.

Sega does not have legal documents detailing fan content. None at all!
Despite this fact the people in charge have given the greenlight for pretty much anything, just not on paper.

https://twitter.com/KatieChrz/status/1391900579966844930?s=20&t=rhAXSem8rWbKlwN84CPxWQ

According to this tweet by the social media manager of Sonic the Hedgehog, the usage should be fine. The fact she mentions "dev work" helps the argument that you have permission. After all, you are training your developer capabilities by working on code.

Then there's also the fact they are fine with fan games. If they are ok with fan games, which is arguably a far more grave case of copyright infringement, then a mod for another game that won't even compete for the same audience should be more than ok.

You therefore, unofficially, have the right to use Sonic the Hedgehog. And if the word of a corporate official means nothing, then I don't know what to say.

Their statement, however, means nothing for other Sega owned brands.

Electronic Arts has no legal documents regarding fan art. Simply a request policy.

EA lets you ask for permission. By going to the link below you can request permission to use any of their owned franchises. Just bear in mind to make it clear you are a fan making a fan creation. There should be no confusion over your intent.
Link: https://help.ea.com/en-gb/help/faq/how-to-request-permission-for-ea-games-content/

I cannot say more than that. Be mindful of what they say, and good luck.

Games that EA owns that you may request:

Overlord
Sims
Spore
Dead Space
MySims
Dragon Age
Peggle
Plants vs. Zombies
Mass Effect

CD PROJEKT RED do explicitly say they don't allow mods of the Witcher, and other brands they have the license to, for other games. But! They do say this matter can be discussed in private. As such, you may be allowed to upload fan creations to the Workshop. Bear in mind that such a permission would be yours and yours alone, and absolutely could never be transferred over to anyone else. They'd have to make their own inquiries.

Rules of note:

Make it clear the work is unofficial.
Don't hurt CD PROJEKT RED or others with the fan content.
You MUST list the following or similar disclaimer on your Workshop page:

This is an unofficial fan work and is not approved/endorsed by CD PROJEKT RED

But remember: permission required first!
legal@cdprojektred.com
This is the email where you may ask for permission. Be formal, be respectful, and make it clear what you're setting out to do.

CD PROJEKT RED has the video game rights to The Witcher and maybe Cyberpunk 2077. If you do ask them about Cyberpunk 2077, please let me know! Because I could not find if they own any sliver of the Cyberpunk IP aside from being allowed to make the game.

Legal document:
https://www.cdprojektred.com/en/fan-content

I will keep all the company names directly under this tab, as there isn't really any purpose to being able to find companies you can't use quickly.

All companies here have in some way or another expressed a direct negative stance, and may have in some cases even written it down in their policies to prevent you from making interactive media based on their brands.

- Innersloth - Among Us and Henry Stickmin
The people behind Among Us strictly state that interactive media based on their brands is prohibited.

- Wizards of the Coast - Dungeons & Dragons and Magic the Gathering
WotC strictly states that you may not contribute their brands to any game format.

- Nintendo - Super Mario, Legend of Zelda, Donkey Kong, Kirby, etc
Nintendo has made no official statement, but they are notoriously strict about their copyright.

- Behaviour Interactive - Dead By Daylight, Scaler the Chameleon, Naughty Bear, etc
Behaviour has strictly stated that you may not use their brands for interactive media.

- Bandai Namco Entertainment - Elden Ring, Pac Man, Tamagotchi, etc
The terms in their legal documents prohibits any and all fan content for any purpose whatsoever.