Nikto web server scanner
Nikto is an Open Source web server scanner which performs comprehensive tests against web servers for multiple items, including over 6700 potentially dangerous files/programs, checks for outdated versions of over 1250 servers, and version specific problems on over 270 servers. It also checks for server configuration items such as the presence of multiple index files, HTTP server options, and will attempt to identify installed web servers and software. Scan items and plugins are frequently updated and can be automatically updated.
Nikto is not designed as a stealthy tool. It will test a web server in the quickest time possible, and is obvious in log files or to an IPS/IDS. However, there is support for LibWhisker's anti-IDS methods in case you want to give it a try (or test your IDS system).
Not every check is a security problem, though most are. There are some items that are "info only" type checks that look for things that may not have a security flaw, but the webmaster or security engineer may not know are present on the server. These items are usually marked appropriately in the information printed. There are also some checks for unknown items which have been seen scanned for in log files.