Browser (e.g. Firefox, Chrome) Manual crawling of the application and support manual testing of the application. Firefox has a number of built-in plugins such as Web Developer and Firebug that can provide easily viewable information on the source including hidden fields and HTML parameters.
Burp Suite Pro Web proxying tool that supports automated crawling, intercept and manipulation of HTTP requests, replay, injections, randomness of session identifiers, etc. The pro version also supports passive and active scanning.
Nikto (Kali distro) Web server vulnerability scanner that can fingerprint the web server and identify any known vulnerabilities with the web server software or installed application components (e.g. Tomcat) residing on the web server.
Nmap (Kali distro) Port scanner that can quickly identify open application ports on the systems as well as fingerprint the services bound to each port. Nmap additionally provides power in the NSE scripts which can probe services for detailed information, e.g. SSL supported ciphers.
Web Inspect Automated vulnerability scanning of web applications and web services. This is particularly useful for large, complex applications.
SQLmap (Kali distro) SQL injection and blind SQL injection tool used to pinpoint and execute proof of concept SQL injections.
Dirbuster (Kali distro) Brute-force directory guessing to find hidden web interfaces (e.g. admin pages, server status pages).