Main ones in bold

General Yugioh Subreddits:
/r/Yugioh - Primary subreddit for discussion
/r/Yugioh101 - Help for new players
/r/YugiohShowcase - For showing off collections
/r/CustomYugioh - Custom card creation
/r/Yugijerk - Shitposting subreddit
/r/YuGiOhMemes - Meme subreddit

Yugioh Market Subreddits:
/r/YGOMarketplace - Buying, selling and trading cards
/r/YGOFeedback - Feedback in relation to Marketplace, inactive
/r/YugiohEconomy - Yugioh market discussion, inactive

Yugioh Game Subreddits:
/r/DuelLinks - For the Yugioh mobile game
/r/YGOLegacyofTheDuelist - Legacy of the Duelist video game
/r/YuGiOhMasterDuel - Master Duel game subreddit

Individual Yugioh Archetype Subreddits: (most aren't very active)
/r/YugiohCounterFairy - Counter Fairy
/r/DarkMagician - Dark Magician
/r/Deskbots - Deskbot
/r/Dinomist - Dinomist
/r/Firekings - Fire King
/r/Frightfurs - Fluffal/Frightfurs
/r/Infinitrack - Infinitrack
/r/Krawlers - Krawler
/r/Lunalights - Lunalight
/r/Madolche - Madolche
/r/MechaPB - Mecha Phantom Beasts
/r/Monarchs - Monarch
/r/Shaddolls - Shaddoll
/r/RANK10TRAINS - Trains
/r/Triamids - Triamid
(if you know of any more of these archetype subs, let me know)