The Side Deck in Yu-Gi-Oh! is one of the most critical features when it comes to the game. The Side Deck is home to 15 cards from outside of your Main Deck that you can use to replace cards inside of it in between games.
This means the Side Deck is one of the most important aspects of the Deck building process. The Side Deck is generally widely different based on what the current meta is. However, some Side Decks cards are so good, they'll almost always be relevant. The ability to control if the player is going first or second can be big swings in games 2 and 3.
Updated January 26th, 2021 by Johnny Garcia: Tons of Yu-Gi-Oh! Sets come out annually, and as such the card pool expands more than any other trading card game out there. Due to the frequency of Set releases and reprints, many decks are introduced or revived that completely change the scope of the meta. Sets like the upcoming Blazing Vortex are expected to make a big impact on the meta, and as such, the cards going in Side Decks are likely going to have plenty of new additions. The next Set is expected to be revealed in the OCG soon, and when that happens the game will change even more.
15 Kaiju Monsters
The best kind of removal in the game for any Monster is using it for a Tribute. Very little cards have protection from being Tributed, and the ones that do aren't generally played often. That's what makes the Kaiju series of Monsters so good.
All of the Kaijus have an effect that Tributes a Monster on the opponent's field to Special Summon them onto their field. While giving the opponent a Monster may seem bad, getting rid of a powerful Monster for a more simple one with no real effect is a fantastic trade-off.
14 Appointer Of The Red Louts
While not at all useful going second, when you know you're going first, Appointer Of The Red Lotus is a phenomenal card. That's why it's perfect for the Side Deck (and awful for the Main Deck).
At the cost of 2000 Life Points and showing your hand to your opponent, you can look at the opponent's hand and Banish a card from there. In the modern game of Yu-Gi-Oh!, so many combos rely on one card, so getting rid of that before they can use it is what makes Appointed Of The Red Lotus so good. It can also get rid of cards that would wipe the board or negate it like Dark Ruler No More and Evenly Matched.
13 Artifact Sanctum
Artifact Sanctum is a fantastic Trap card that when activated, Special Summons an Artifact Monster from the deck. If it gets destroyed before its activated, Artifact Sanctum can also target and destroy a card on the field.
While not many Artifacts care to be Special Summoned, the one that does is what makes Artifact Sanctum so good. That would be Artifact Scythe, which when Special Summoned during the opponent's turn prevents them from Summoning any card from the Extra Deck. In modern Yu-Gi-Oh!, the Extra Deck is so important, so shutting that down is an amazing effect.
12 Imperial Order
Imperial Order is one of the oldest cards in the game that still sees play in the modern game. Originally released in 2002's Pharaoh's Servant Set, the card is currently limited to one copy per deck. When activated, Imperial Order negates all Spell card effects.
Spell cards are the most important kind of cards in Yu-Gi-Oh! and plenty of decks rely on them to get their plays going. While it does affect you as well, due to the Floodgate nature of it, your field will likely already be established so it won't harmfully affect you.
11 Ghost Belle & Haunted Mansion
Ghost Belle & Haunted Mansion is a card that's been in and out of the meta since its release in the Flames of Destruction Set. It is essentially the opposite of Ash Blossom & Joyous Spring. Rather than stopping cards moving from the deck, Ghost Belle & Haunted Mansion stops cards from moving from the Graveyard.
By discarding Ghost Belle & Haunted Mansion, it can negate the activation of any card that moves a card from the Graveyard to anywhere else. These include Special Summoning from there, adding a card from there to the hand, and Banished a card from the Graveyard.
10 The Winged Dragon Of Ra – Sphere Mode
What is the best God Card by a wide margin, The Winged Dragon Of Ra – Sphere Mode is one of the best ways to guarantee the opponent's Field is dismantled. While awful against Control Decks, this is why it's such a good card to keep in the Side Deck to put in when up against Combo Decks that end up on big boards. The Winged Dragon Of Ra – Sphere Mode will Tribute 3 Monsters at the cost of losing the Normal Summon. Tributing Monsters is the best form of removal, as it gets around any kind of protection a Monster may have.
9 Anti-Spell Fragrance
Anti-Spell Fragrance is the anti-Pendulum card. Anti-Spell Fragrance requires Spell cards to be Set for a turn before using them. Not only does this hinder many Decks, as many of them rely heavily on Spell cards, it completely prevents Pendulum Monsters from being placed on the Scales.
Since Pendulums can't be Set, this means they are only usable as Monsters. While being good on its own, the fact Anti-Spell Fragrance can shut down an entire mechanic permanently while on the Field is what makes it such a fantastic Side Deck choice.
8 Summon Limit
Summon Limit is a fantastic card that prevents either player from Summoning more than twice per turn, and negated Summons are counted towards that limit. Summon Limit is better left in the Side Deck since it has little use going first and against Control Decks. However, when the player can guarantee they go first, Summon Limit more often than not can completely shut down the opponent's turn, which can then guarantee a win on the next turn. While it does affect its controller, Summon Limit isn't going to be activated until a board is already established, so they would not care for its effect.
7 Artifact Lancea
Artifact Lancea, depending on the meta, is one of the best Side Deck options out there. During the opponent's turn, the player can Tribute it from their Hand or Face-Up Field and will prevent either play from being able to Banish cards that turn. Artifact Lancea is so powerful in the Side Deck because some Decks such as Orcust and Thunder Dragons heavily rely on Banishing for their Deck to function. In a pinch, it can even be used against a card like Evenly Matched, negating it and causing the opponent to lose their Battle Phase in the process.
6 Super Polymerization
Super Polymerization is one of, if not, the strongest Fusion Spell in the game. At the cost of discarding 1 card, Super Polymerization can fuse Monsters from either Field together as Fusion Materials. It also cannot be responded to by any cards.
This is great for getting rid of Monsters on the opponent's Field, as most often the Fusion Materials will be taken exclusively from there. Mixed with cards like Mudragon Of The Swamp or Starving Venom Fusion Dragon, the player will be able to get a strong Monster out of the exchange.
5 Red Reboot
Red Reboot is one of the strongest answers to Trap Cards in the entire game. When activated, it can negate a Trap Card at the cost of the opponent being able to Set another Trap Card from their Deck. The Tradeoff for this is the opponent will not be able to activate any other Trap Cards for the rest of the turn. This makes Red Reboot great, but what makes it fantastic is it can be activated from the Hand at the cost of half of the player's Life Points.
4 Nibiru, The Primal Being
Nibiru, The Primal Being is one of the strongest counters to Combo Decks. If the opponent Summons five or more Monsters during their turn, Nibiru, The Primal Being can be activated, causing all the Monsters on the Field to be Tributed. This gives the opponent a Token with Attack and Defense equal to the combined stats of all Tributed Monsters. This also leaves its user with Nibiru, The Primal Being on the Field, a powerful 3000 Attack Monster. If timed right, Nibiru, The Primal Being can shut down the opponent's turn, leaving them with nothing but a Token.
3 Evenly Matched
Evenly Matched has the most powerful Field Wiping ability in all of Yu-Gi-Oh! At the end of the Battle Phase, Evenly Matched forces the opponent to Banish cards from their Field Facedown, until they control the same amount of cards.
If no cards are controlled, Evenly Matched can be activated from the Hand, which can leave the opponent with only one card on the Field. The tradeoff of losing the Battle Phase is more than worth it when the opponent's Field can be permanently taken care of. Its biggest weakness is when going first. It isn't going to do a whole lot, which is why it's a staple Side Deck card.
2 Dark Ruler No More
Dark Ruler No More is the strongest full board negate in the game. It will negate the effects of all face-up Monsters on the Field, and no Monsters can respond to its activation, only Spell and Trap Cards. The tradeoff to this is the opponent will take no damage for that turn. Odds are, they've used most of their resources making the board, so after taking care of the Monsters, they'll be hard-pressed to recover. Dark Ruler No More is the strongest going second card against Combo Decks, which is why every Side Deck should have copies of it.
1 Lightning Storm
Lightning Storm is an incredibly powerful going second card, and one that is good against both Combo and Control Decks. So long as its user has no face-up cards on the Field, Lightning Storm can either destroy all Spell and Trap Cards or all Attack Position Monsters the opponent controls. This makes Lightning Storm incredibly versatile. Not limited by being only good against certain Decks, a wipe of backrow cards or Monsters will rarely ever not be useful. Since there won't be anything on the Field going first, Lighting Storm is best used in the Side Deck. It can completely dismantle boards going second, especially when combined with other cards such as Dark Ruler No More.