There are several well-known penetration testing methodologies and standards.
The Open Web Application Security Project (OWASP) has developed a widely used set of standards, resources, training material, and the famous OWASP Top 10 list, which provides the top ten web vulnerabilities and the methods to detect and prevent them.
The Open Source Security Testing Methodology Manual (OSSTMM) is a widely used methodology that covers all aspects of performing an assessment. The purpose of the OSSTMM is to develop a standard that, if followed, will ensure a baseline of test to perform, regardless of customer environment or test provider. This standard is open and free to the public, as the name implies, but the latest version requires a fee for download.
The Information Systems Security Assessment Framework (ISSAF) is a more recent set of standards for penetration testing. The ISSAF is broken into domains and offers specific evaluation and testing criteria for each domain. The purpose of the ISSAF is to provide real-life examples and feedback from the field.