A hypothesis is an assumption, an idea that is proposed for the sake of argument so that it can be tested to see if it might be true.
In the scientific method, the hypothesis is constructed before any applicable research has been done, apart from a basic background review. You ask a question, read up on what has been studied before, and then form a hypothesis.
A hypothesis is usually tentative; it's an assumption or suggestion made strictly for the objective of being tested.
A theory, in contrast, is a principle that has been formed as an attempt to explain things that have already been substantiated by data. It is used in the names of a number of principles accepted in the scientific community, such as the Big Bang Theory. Because of the rigors of experimentation and control, it is understood to be more likely to be true than a hypothesis is.
In non-scientific use, however, hypothesis and theory are often used interchangeably to mean simply an idea, speculation, or hunch, with theory being the more common choice.
Since this casual use does away with the distinctions upheld by the scientific community, hypothesis and theory are prone to being wrongly interpreted even when they are encountered in scientific contexts—or at least, contexts that allude to scientific study without making the critical distinction that scientists employ when weighing hypotheses and theories.
The most common occurrence is when theory is interpreted—and sometimes even gleefully seized upon—to mean something having less truth value than other scientific principles. (The word law applies to principles so firmly established that they are almost never questioned, such as the law of gravity.)
This mistake is one of projection: since we use theory in general to mean something lightly speculated, then it's implied that scientists must be talking about the same level of uncertainty when they use theory to refer to their well-tested and reasoned principles.
The distinction has come to the forefront particularly on occasions when the content of science curricula in schools has been challenged—notably, when a school board in Georgia put stickers on textbooks stating that evolution was "a theory, not a fact, regarding the origin of living things." As Kenneth R. Miller, a cell biologist at Brown University, has said, a theory "doesn’t mean a hunch or a guess. A theory is a system of explanations that ties together a whole bunch of facts. It not only explains those facts, but predicts what you ought to find from other observations and experiments.”
While theories are never completely infallible, they form the basis of scientific reasoning because, as Miller said "to the best of our ability, we’ve tested them, and they’ve held up."
