1. Analyze the Leader's type
This is key. I will use the Normal Type for my example. Now we all know that Fighting is Normal's only weakness, right? Good, Pokemon 101. Now let me take that a little further and analyze how a Normal leader overcomes that weakness. Seeing that Fighting is resisted by Poison, Psychic, Ghost (Takes nothing), Bug and Flying, it is apparent that the wildcards will be of those types. So let me break down what this means to you as a challenger. If your team consists of 3-4 Steels, not only do you resist my STAB move, you also resist the STAB of my wildcards. Then you have 2-3 open spots for set up, things that disrupt teams, etc. Finally, you need to know what can super effectivly counter wildcards. If it is something very bulky, chances are it could be used to counter. Especially something like Dusknoir or Bronzong (in terms of a Normal team) So in conclusion:
-Make sure you aren't excesivly using resists. (Excessive as in 3-4).
-Be sure to know the weaknesses of a type and the wildcards that come along with those weaknesses.
-Know your type chart. You need to know what resists what and what is Super Effective against what.
2. Know the Leader's Type
This is different than analyzing a type. Let me use the Electric Gym as an example. The first thing that popped into my head when I played with making an Electric team way back was that there were very limited Physical Attackers in the game. This means a very potent Special Wall, such as Blissey or Snorlax, could take on an Electric team fairly well. True the leader has wildcards and could use a physical attacker to counter BLissey or Lax, but countering a wall is pretty hard, since you aren't actually countering attacks, moreover status conditions or really bulky Pokemon (Blissey and Lax respectivly). So, in conclusion:
-If a type leans to a specific stat (be it SpAtk, Atk, Def, SpDef) make sure your team isn't excessivly dominant in the opposing stat (SpDef, Def, SpDef, Atk respectivly)
3. Last but not least: Know your Combinations!
Yes, a moveset, item and EV spread can definatly be considered part of countering. I'm going to use a Poison team as an example for this one. Poison's counters are Psychic and Ground (However I will focus on the Ground aspect as there is no move that impacts the Psychic weakness). This isn't all too bad, seeing as there are a bunch of Fliers, Poison or not. However, when a team comes in that is based around Gravity, we have a problem. Not only are the Levitators and Fliers brought down, but now there is STAB (Or Strong) Super Effective move that can hit every Pokemon! So in conclusion:
-Take note of the Pokemon within the type
-Make sure there isn't a move in your team that can wreck havoc on the opposing team, even if it is a Choice Scarf, or special EV spread, something can do massive amounts of damage
I want you guys to realize that all of these factors come into play when defining a counter team. Those of you who pay real close attention can see multiple overlaps in the 3 issues. So basically, when making a team to challenge the league, or even when debating whether your match (aimed at leaders) was against a counter team, use these guidelines. However, use these as guidelines, NOT as rules!
Credit for this Guide goes to Hauntershadow92 (of Sppf Forums)