Found a good article on side decks but it pretty much focuses on the meta decks and how to Use cards against them.
"Learning how to use your Side Deck can decide whether you win or lose at a tournament.
Side Deck basics are easy. You can have up to 15 cards in your Side Deck. After you finish the first Duel in a Match, you can take cards out of your Deck (Main Deck or Extra Deck) and swap them with cards in your Side Deck. At this point, you know what kind of Deck you’re playing against. So you can use your Side Deck to fix up your Deck in the middle of the Match, and put in cards that work best against your opponent’s Deck.
Here are some strong cards to keep in your Side Deck for use against some of the most common theme Decks you’ll see these days.
Side Decking vs. Lightsworn
It’s important to stop a Lightsworn Deck from filling up its Graveyard with monsters. Whenever “Kycoo the Ghost Destroyer” inflicts damage to your opponent, you can remove 2 monsters in their Graveyard from play. Using this effect to remove Lightsworn monsters from play can prevent your opponent from Summoning “Judgment Dragon,” which requires 4 different Lightsworn monsters in the Graveyard. You can also remove monsters like “Judgment Dragon” or “Celestia, Lightsworn Angel” from the Graveyard to keep your opponent from getting them back in their hand.
“Kycoo the Ghost Destroyer” also stops your opponent from removing cards in their Graveyard from play, which means they can’t use “Necro Gardna” to block your attacks. If you face a Twilight Deck using “Chaos Sorcerer,” they can’t remove a LIGHT and DARK monster from play to Summon it, either.
The card that Lightsworn players fear most is “Light-Imprisoning Mirror” since it blocks all LIGHT monster effects from working. If your Deck doesn’t have many LIGHT monsters in it, you should definitely have 3 “Light-Imprisoning Mirrors” in your Side Deck, in case you face a Lightsworn Deck.
Side Decking vs. Gladiator Beasts
“Mirror of Oaths” is a card from Raging Battle that is very strong against Gladiator Beasts. When your opponent Special Summons a monster from their Deck, you can activate “Mirror of Oaths” to destroy that monster, plus you get to draw a card! Gladiator Beasts are all about tagging monsters in and out of the Deck, so “Mirror of Oaths” can stop their combos dead in their tracks.
Another good tactic is to stop a Gladiator Beast player from using any of their monster effects. “Skill Drain” negates the effects of every monster card on the field, so it’s another great candidate to use against Gladiator Beasts.
Side Decking vs. Blackwings
“Bottomless Trap Hole” is a great card to use against lots of Decks. But even if you don’t use it in your Main Deck, consider using 2 copies in your Side Deck to use against Blackwings. Blackwing Decks rely on “Black Whirlwind” to search for more Blackwings from their Deck. But if you can destroy a Blackwing when it’s Summoned (using your “Bottomless Trap Hole,” for example), your opponent won’t get to search for another Blackwing with “Black Whirlwind.”
“Black Whirlwind” also won’t work if the Blackwing monster is flipped face-down when it’s Summoned, so you could also try “Book of Moon” to keep “Black Whirlwind” from working. Most Blackwing monsters have very low Defense Points too, so you should be able to destroy them in battle with your own monsters.
Even if you can’t stop “Black Whirlwind,” you can still stop your opponent’s Special Summons with “Royal Oppression.” Blackwing Duelists can Special Summon 2 or 3 monsters in one turn, but you can stop all that with “Royal Oppression,” so they’ll just have their 1 Normal Summon each turn.
You can also try “Summon Limit,” which stops players from Summoning more than 2 monsters per turn. Blackwing Decks can use their Normal Summon and Special Summon to set up a Tuner and a non-Tuner in the same turn. But if “Summon Limit” is on the field, they won’t be able to Synchro Summon that turn, too.
General Side Deck Cards
There are many cards that work well against multiple Decks:
“Lightning Vortex” is good against Decks that Special Summon lots of monsters, like Blackwings, Lightsworn, and Zombies.
“Royal Decree” and “Jinzo” are great if your opponent plays a lot of Trap Cards.
“Dimensional Fissure” and “Banisher of the Radiance” can beat Graveyard-based Decks.
There’s a card out there to beat every other card, and using your Side Deck gives you access to the cards you need. Sometimes your Side Deck can get you out of Matches that seem impossible to win, so don’t be afraid to use it. Try out lots of different cards in your Side Deck and see what works best for you."
Source: Konami.com/yugioh/articles