A charge that is sometimes made against evolution, for example, is that it is "just a theory." Evolutionists are quick to point out that such an argument shows that the idea of "theory" is misunderstood. Let's seek to understand it, then.
Science seeks to understand how things work in the universe. In order to do so, we must take things in nature and formulate them in ways that humans can understand. There is always this disconnect between nature's reality, and humanity's nature. You can sense that sunlight on your skin is warm, but the thought in your mind of warmth and warmth itself are two different things.
A theory is, in my words, an attempt at a descriptive abstraction of nature in a way that humans can understand. The disconnect requires that any human description of nature be an abstraction. Because of this, any theory is only as good as our observations of nature. Imagine if everything you see is in shades of blue, and that is all you've ever known. You might develop ideas on how light works based on your observations. Of course, any explanation you give for how nature works will certainly be wrong, since we know that world is not only in shades of blue. Or is it? What is "blue," anyway? How can we know for certain that we all don't suffer from defective senses? But then again what does it matter? We must conclude that science is not concerned about nature in itself, but only about our perception of nature. That is, really, the best we can do.
Now, I carefully crafted my words to say "an attempt." Note well this quote of Stephen Hawking:
"All we ever know is our models, but never the reality that may or may not exist behind the models and casts its shadow upon us who are embedded inside it. We imagine and intuit, then point the finger and wait to see which suspect for truth turns and runs. Our models may get closer and closer, but we will never reach direct perception of reality's thing-in-itself." [As given by George Zebrowski, "The holdouts," Nature, Vol. 408, 14 Dec 2000]
Theories are what science does; they are all it has. A theory can never be proved, it can only be disproved. If an explanation of nature withstands all we throw at it to disprove it, we then tend to think it is true.
A very important facet to a theory is that it can make verifiable predictions of how nature should work in a certain situation. If such predictions turn out to be true, we tend to think even more that the theory is true. For example, Einstein's general relativity predicted that light should bend around the sun. Upon observation, this was confirmed (Einstein's calculated numbers fell within the observation's tolerance), much to the excitement of the scientific community.
So when something is granted the title of Theory, we must know that it has been rigorously tested and has been found to be a very accurate description of reality. The charge that evolution is "just a theory" is the same as charging it as "just science."