The word theory has a number of distinct meanings in different fields of knowledge, depending on their methodologies and the context of discussion.
In science, a theory is a mathematical or logical explanation, or a testable model of the manner of interaction of a set of natural phenomena, capable of predicting future occurrences or observations of the same kind, and capable of being tested through experiment or otherwise falsified through empirical observation. It follows from this that for scientists "theory" and "fact" do not necessarily stand in opposition. For example, it is a fact that an apple dropped on earth has been observed to fall towards the center of the planet, and the theories commonly used to describe and explain this behavior are Newton's theory of universal gravitation (see also gravitation), and the theory of general relativity.
In common usage, the word theory is often used to signify a conjecture, an opinion, or a speculation. In this usage, a theory is not necessarily based on facts; in other words, it is not required to be consistent with true descriptions of reality. This usage of theory leads to the common incorrect statements. True descriptions of reality are more reflectively understood as statements which would be true independently of what people think about them.
According to the National Academy of Sciences,
"Some scientific explanations are so well established that no new evidence is likely to alter them. The explanation becomes a scientific theory. In everyday language a theory means a hunch or speculation. Not so in science. In science, the word theory refers to a comprehensive explanation of an important feature of nature that is supported by many facts gathered over time. Theories also allow scientists to make predictions about as yet unobserved phenomena."
http://en.wikipedia.org/wiki/Theory