Wapiti

Wapiti allows you to audit the security of your web applications. It performs "black-box" scans; i.e., it does not study the source code of the application but will scans the webpages of the deployed webapp, looking for scripts and forms where it can inject data. Once it gets this list, Wapiti acts like a fuzzer, injecting payloads to see if a script is vulnerable.

Wfuzz

Wfuzz is a tool for bruteforcing Web Applications, it can be used for finding resources not linked (directories, servlets, scripts, etc), bruteforcing GET and POST parameters for different kinds of injections (SQL, XSS, LDAP, etc.), bruteforcing form parameters (user/password), fuzzing, and more.

Skipfish

skipfish is an active web application security reconnaissance tool. It prepares an interactive sitemap for the targeted site by carrying out a recursive crawl and dictionary-based probes. The resulting map is then annotated with the output from a number of active (but hopefully non-disruptive) security checks. The final report generated by the tool is meant to serve as a foundation for professional web application security assessments.

w3af

W3af is an extremely popular, powerful, and flexible framework for finding and exploiting web application vulnerabilities. It is easy to use and extend and features dozens of web assessment and exploitation plugins. In some ways it is like a web-focused Metasploit.