Ammonite!

Nikto is an Open Source (GPL) web server scanner which performs comprehensive tests against web servers for multiple items, including over 6400 potentially dangerous files/CGIs, checks for outdated versions of over 1000 servers, and version specific problems on over 270 servers.

Burp Suite is an integrated platform for performing security testing of web applications. Its various tools work seamlessly together to support the entire testing process, from initial mapping and analysis of an application's attack surface, through to finding and exploiting security vulnerabilities.

Audit your website security and web applications for SQL injection, Cross site scripting and other web vulnerabilities with Acunetix Web Security Scanner. Download Free Edition!

w3af is a Web Application Attack and Audit Framework

Netsparker is the only False-positive-free web application security scanner. Simply point it at your website and it will automatically discover the flaws that could leave you dangerously exposed.

Websecurify is a powerful web application security testing environment designed from the ground up to provide the best combination of automatic and manual vulnerability testing technologies.

Firefox add-on that lets you change headers and request parameters before they're sent to the server. Unlike proxy request modifiers, it's integrated into the browser, so it has no problem with HTTPS connections, client authentication certificates, or other features that the browser supports.

Intruder is a proactive security monitoring platform for internet-facing systems.

Golem Security Scanner is a powerful and intuitive website security scanner which uses a combination of proprietary and open source scanners to maximize the scan findings. Much less expensive for the paid version than other providers, with a free option which scans a portion of the site.