This question seems to bother a lot of people. Many people believe that since this is hard to understand the Bible cannot be right. But the problem isn't that the Bible is wrong, it is that people don't want to believe it.

The probable answer to where Cain got his wife was that he married a sister. I know what you are saying "That's wrong!" And you are right, that today it is wrong. But God did not command people not to marry close relatives until the days of Moses (more than 2000 years later). One reason God probably gave this command is that it is very harmful for close relatives to have children, this would cause a lot of disease and many birth defects. This is because of diseases and deformities (like a missing arm, or bad eyesight, etc..) In the beginning when God made mankind this was not true. Most of these diseases and problems probably did not begin till after Noah's flood.

Another reason is that at the very beginning there would be no one else to marry except relatives. Also remember that Adam lived 930 years - he could have had hundreds of children during that time!

Genesis 5:4-5
After he begot Seth, the days of Adam were eight hundred years; and he had sons and daughters. So all the days that Adam lived were nine hundred and thirty years; and he died.