[omginternets]

Many of the answers here are pointing to methods, but I take this question as more fundamental.

Epistemologically, causation is the intersection of three things:

1) Temporal precedence

2) Covariance (i.e. correlation)

3) Absence of likely alternative explanations

Number 3 is by far the trickiest. Our inability to definitively rule out all possible alternatives means one has to resort to inference where causation is concerned.