Scoring is the the act of creating a line or depression in the paper that will help the paper fold. This is the best way to create a fold in card stock or any somewhat thicker paper.
For example if you want to make a folded card it is best to score the card where it is going to fold and then fold it. If you simply fold it your crease may look very unprofessional or the paper may even crack.
You can score paper using a very dull knife (like a butter knife) and a ruler. However you accomplish the score it needs to be deep enough that the paper will want to fold along that line easily.