This here is a soon to be guide about spell counters and how to effectively use them; I will update the original post as time goes along. I may miss afew monsters or supporting cards; if so please inform me.
Note: This guide in the present state will possibly only help begginers.

SC=Spell counter

Spell Counters

What are they?

Spell counters are special counters placed on certain spellcasters due to an abbility. However only certain effect spellcaster monsters can use spell counters can use them; namely one of the most commonly used spell counter monster is Breaker The Magical Warrior.

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What they do and how to gain them?

Spell counters have different effects according to the monsters that they are placed on and can be generated by different effects.

Examples:

SC use: Card destruction / ATK boost
Gained: By being summoned

Breaker the magical warrior:(1600/1000)
Can hold 1 spell counter maximum. He gains the spell counter when he is summoned and it alows him 2 abbilitis
1: while he has the spell counter he gains 300 atk points
2: tribute the spellcounter to destroy 1 spell or trap card on the field thus returning his attack poiunts to normal.

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SC use: Level up
Gained: Drawing a card

Silent magician lv.4:(1000/1000)
Can hold 5 spell counters max. She gains them when your oppoment draws a card. When she has 5 you can Level her up to LV.8

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SC use: Multiple uses
Gained: By activation of a spell card. (Yours and your oppoments)

I will not give an example here as there are multiple monsters that gain a spell counter when summoned so I will list 5.

Royal magical library:(0/2000)
This card can hold 3 spell counters max. You can sacrafice all three during your turn to draw an extra card (the monster stays on the field). This can help speed the deck alittle.

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Mythical beast cereberus:(1400/1400)
Unlike the other monsters up until now this card can hold an infinite amount of spell counters. Like breaker the magical warrior this card gains an attack boost but of 500 points for each spell counter; however this may only be good as a defence of sorts as after cereberus attacks he loses all spell counters.

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Blast magician:(1400/1700)
Like cereberus he can hold an infinite amount of spell counters his abillity is quite different to most other spell counter monsters. You may chose to sacrafice any number of spell counters on him to destroy a monster whose atk is equal to or less than 700 times the number of sacraficed spell counters.

remove any number of spell counters from this monster to destroy a monster with ATK points equal to 700 * the number of removed spell counters

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Skilled dark magician:(1900/1700)
This card can only hold 3 spell counters but you can sacrafice this card with 3 spell counters to special summon 1 dark magician from your hand, deck or graveyard. Some spellcaster decks use this a beat down or to confuse your oppoment into wasting their destruction cards.

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Skilled white magician:(1700/1900)
Same as above except you can summon buster blader from your hand deck or graveyard.

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Cards that let you gain spell counters.

Pitch black power stone:trap
When you play this card place three spell counters on it. Once per turn you can move 1 spell counter from this card to an appropriate monster on your side of the field.

This helps you get spell counters with the need of a spell card or other reorces to gain them. You reuse breaker's ability with this once a turn for three turns if it stays on the field that long.

Apprentice magician:(400/800)
When you normal, flip or special summon this card you can place a spell counter on 1 face up monster that can hold spell counters. As alittle bonus when this card is destroyed you can set 1 level2 or lower spellcaster from your deck on your side of the field. This is anouther way to gain spell counters easy and then keep field presence. People call it the 'apprentice engine' and use it various decks.

Magical Plant Mandragola:(500/200) (level 2 spellcaster)
Flip: Place 1 spell counter on every face up monster that you can put a spell counter on.
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Cards that destroy spell counters.

Exhausting spell:trap
Destroy all spell counters on the field.

There plain and simple.

Counter Cleaner:normal spell
Destroy all counters on the field.

Yep ALL counters; spell counters, clock tower prison counters, any others.

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Decks that use spell counters or speed usage.

There are various ways to build a spell counter deck.

Theres a burn version that uses dark eradicator warlock and normal spells to deal damage while you gain spell counters. Magical explosion also works. I heard of someone saying a diamond dude turbo would work with a burn version.

Dark magician can be used but he is usualy sacrficed for dark eradicator warlock or used in dedication through light and darkness.

You could even make a beat down of sorts or a control deck but these will require other spellcaster or non-spellcaster cards.

you could fit them into a dark paladin deck.

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Other notable spellcasters.

Hanibal necromancer:(1400/ )
When you normal summon this card put 1 spell counter on it. You may remove a spell counter from this card to destroy 1 face up trap card on the field.
While possibly only seen in the video games he does use spell counters so he is mentioned.

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Ledgendary Flame Lord:(2400/2000) (Ritual Monster)
Every time a spell card is activated place a spell counter on this card (MAX.3). Remove 3 spell counters from this card to destroy every card on the field except this card.

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Armor Exe:(2400/1400) level 4 rock
This card cannot attack the same turn it is normal, flipped or special summoned. During your and your oppoments standby phase remove one spell counter on the field if you do not this card is destroyed.

While not a spellcaster it does use spell counters to stay on the field

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Weaknesses of certain cards.

Pulling the rug and solemn judgeemet can rid of some of these monsters quite easily along with other removal cards.

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Supporting cards.

As they are mostly spellcasters they get all the spellcaster support as well as from other cards that use spell counters. Most spell cards aswell.

Miracle Restoring:Trap
Remove 2 spell counters on your side of the field to special summon 1 'dark magician' or 'buster blader' from your graveyard to your side of the field.

Anti-Spell:Counter Trap
Remove 2 spell counters from your side of the field to negate the activation of a spell card and destroy it.

Mega Ton Magical Cannon: Normal Spell
Remove 10 spell counters from your side of the field to destroy all cards on your oppoments side of the field.

Spell absorbtion: continous spell
When a spell card is activated you gain 500 lp and with the number of spell cards in a spell counter deck it comes in handy.
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Cards that slow the deck.

Tower of Babel:continuous trap
Every time a spell card is activated place a spell counter on this card. When the forth spell counter is placed on this card destroy it and deal 3000 points of damage to the player who activated the spell card at that time.

can be good or bad bottom line is it can slow decks down.

Horus the black flame dragon LV.8:(3000/2400)

gives the user control of spell cards

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Well there it is it took me a long time to write so please don't trash it.
Note: This is only the begining soon this guide will be complete.