It can mean have a good day, week, weekend or any other period of time. It is used to informally express good wishes for the person being spoken to. I could say "Have a good day" or "Have a good one." The second would be less formal, usually said to someone you are aquainted with.

It can also refer to a particular activity one is about to take part in. For example, if I was about to go out for the evening then a friend may say "Have a good one" referring to that acitivity.

It's generally a substitute for "Have a good day." It is informal but it can also simply be the case that the person using it speaks informally to everyone.

doohsam, that's the same idea as "have a good day." If one were partaking in a particular activity, such as a wedding or picnic, one wouldn't say "have a good one." They would say "have a nice picnic" or "Have fun at the wedding", something more specific along those lines.