Encounters are a way of sorting combat stats based on different encounters instead of just showing everything at once. An encounter is a fight in game, like a attempt on a boss in a raid.

Example of a encounter list shown in GuildStats.net

Tips and tricks:

The encounters have names based on what fought in that fight.
Trash <number> - Regular NPC`s in the encounter.
PVP <number> - Only players where involved in this encounter.
Boss <name of boss> - You fought a boss fight.

The number behind the encounter name increases based on the total number of encounters