The similarity of the words is no doubt the reason they are confused. The first syllable is pronounced the same in both, and both contain a /sh/ sound:
An important difference, and one that should point a speaker to the correct word, is the fact that they function as different parts of speech.
conscious (adjective): having knowledge or awareness; able to perceive or experience something. Example of correct usage:
In rare cases, patients don’t quite drop off completely and remain just conscious enough to feel pain.
conscience (noun): the sense of right and wrong as regards things for which one is responsible. Example of correct usage:
Under the right conditions, the vast majority of people act as if they have a conscience that causes them to act ethically and look out for others’ interests.
Here are some examples of misuse on the Web:
Incorrect: When your conscious is clear does that mean you are innocent?
Correct : When your conscience is clear does that mean you are innocent?
Incorrect: He remained conscience the whole ride to Kandahar Air Field.
Correct : He remained conscious the whole ride to Kandahar Air Field.
Contributing to the confusion between conscious and conscience is a stylistic device found in discussions of ethics and morality. Writers on these subjects often use the phrase, “a conscience decision” to mean “a decision based on conscience.” For example:
Every clinical judgment is configured within a premise of conscience. It was from this stance that a conscience decision was enacted.
This expression echoes the common idiom “to make a conscious decision,” which means, “to decide with one’s full attention.” A better choice would be “an ethical decision.”
Here’s an example of “a conscious decision” used correctly:
In the last few years, neuroscience experiments have shown that some “conscious decisions” are actually made in the brain before the actor is conscious of them.
Bottom line: If the meaning has to do with being awake, use conscious. If it has to do with knowing right from wrong, use conscience.