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Metacognition is basically thinking about thinking, or the ability to critically analyze why one is thinking their thoughts. Metacognition is also being able to understand what they are doing, their mental processes, etc. For example, being able to critically analyze why one is doing a certain action is an example of metacognition.
Some examples of metacognition include meta-memory (including recognition of the fallibility of memory), monitoring one's learning/understanding, theory of mind, and evaluating one's own beliefs and behaviors. It is often regarded as synonymous with executive functions or second order thinking, in contrast with first order thinking which is more intuitive and automatic.
Metacognition is relevant to understanding and critiquing various religious and pseudoscience claims as skepticism and reconsideration of one's ideas requires the ability to determine whether an idea has merit. Theory of mind, for example, allows one to consider the fact that for whatever reason other people hold an alternative views of the universe and the reasons they might have for doing so. Metacognition also allows one to recognize the errors people often make in pattern detection and attribution of causality.