"Web Application Vulnerability Scanner: An automated security program that searches for software vulnerabilities within web applications." - Web Application Security Consortium Glossary
Web Application Security Scanners will check a website's applications for common security problems such as Cross Site Scripting, SQL Injection, Directory Traversal, Misconfigurations, and remote command execution vulnerabilities. Typically Web Application Security scanners will also check for vulnerabilities in your Web Server, Proxy, Web Application Server, and Web Services.
Open Source Web Application Security Scanners: