Super Effective refers to a Move that deals more than normal damage to a Pokémon.
When a Move is used on a Pokémon in battle, it may deal normal damage, increased damage (Super Effective) or less damage (Not Very Effective). This is determined by the Type of Move used and the Type of Pokémon the Move is used on, also known as Type Effectiveness.
Certain Pokémon Types are more vulnerable to specific Types of damage. For example, Squirtle is in a battle with Charmander. It decides to use Water Gun, which happens to be a Water Type Move. Being that Charmander is a Fire Type Pokémon it is weak against Water and therefore it will take extra damage from the attack.
If a Pokémon Type is weak against a Move, "Super Effective" will appear on the screen after the attack lands.