The methodology section or methods section tells you how the author(s) went about doing their research. It should let you know a) what method they used to gather data (survey, interviews, experiments, etc.), why they chose this method, and what the limitations are to this method.

The methodology section should be detailed enough that another researcher could replicate the study described. When you read the methodology or methods section:

• What kind of research method did the authors use? Is it an appropriate method for the type of study they are conducting?
• How did the authors get their tests subjects? What criteria did they use?
• What are the contexts of the study that may have affected the results (e.g. environmental conditions, lab conditions, timing questions, etc.)
• Is the sample size representative of the larger population (i.e., was it big enough?)
• Are the data collection instruments and procedures likely to have measured all the important characteristics with reasonable accuracy?
• Does the data analysis appear to have been done with care, and were appropriate analytical techniques used? 

A good researcher will always let you know about the limitations of his or her research.