This the misconception that I am confronted with the most, so I will deal with it first. Though I have dealt with this before, that first post was somewhat verbose. I will endeavour to keep this one more concise.
In popular usage, the word “theory” means an idea, or a notion, that explains some phenomenon. It does not involve any sort of analysis, so any explanation can be labelled a “theory” of this type. For example, one might say “I have a theory as to why the other subway train always arrives first. You see, the UFO people set the schedules as a means of psychological torture, to destabilize our society and facilitate a takeover”.
In science, the term “theory” also means an explanation, but one that is built upon empirical observation, and that has been tested repeatedly, and refined and tested again. If the explanation fails these tests, it is rejected. If it passes – that is, it can successfully be used to make predictions of the outcome of controlled experiments – it can be called a theory. In science, the phrase “just a theory” is an oxymoron.
For more on “theory”, see the following Wikipedia articles:
Of course, willfully closed-minded zealots will simply respond with “but it’s just a theory!”