What is considered a "primary reference" and how does it differ from other sources? I checked the web and I still have questions.
What is considered a "primary" resource can vary between disciplines. Since I usually get this question in association with psychology or the health sciences, I am going to assume that you are asking in relation to these.
A primary source would be the original published research of an individual or group. They have posed a questions, designed a method to test the question, conducted research based on the method, and have drawn conclusions as to what their findings might mean.
The goal then is to have it published in a peer-reviewed or scholarly journal. To be published means that a jury of peers, experts in the field, read the research and consider it valid and in need of further discussion. Once published the research is then available to the greater professional world for critique.
Science is based on replicability - therefore the way the research was conducted (the method) must be part of the published article. If others use the same method to conduct research and can't replicate the same results, then it is possible the method was flawed. If the method was flawed then so are the results.
So, the short of it is. In the social & health sciences, a pieces of primary research must have a methods or methodology section included.
Others forms of journal literature exist, such reviews of literature or editorials, but these will never have a methods section (though they are considered part of the scholarly journal literature).