In March 2010 Google released its automated web application security reconnaissance tool Google Skipfish.
The official Skipfish website only offers Skipfish as uncompiled download. Compiling Skipfish on Linux platform is straigthforward, but I didn’t find the same for compiling Skipfish in Cygwin on Windows. To save you some headaches, the guys at Information Security Short Takes blog offer the compiled Windows binaries for download:
http://www.shortinfosec.net/2010/03/compiling-latest-skipfish-for-windows.html
Google Skipfish command line options:
C:\skipfish>skipfish.exe --help
skipfish version 1.29b by <lcamtuf@google.com>
skipfish: unknown option -- -
Usage: skipfish [ options ... ] -o output_dir start_url [ start_url2 ... ]
Authentication and access options:
-A user:pass - use specified HTTP authentication credentials
-F host:IP - pretend that 'host' resolves to 'IP'
-C - append a custom cookie to all requests
-H - append a custom HTTP header to all requests
-b (i|f) - use headers consistent with MSIE / Firefox
-N - do not accept any new cookies
Crawl scope options:
-d max_depth - maximum crawl tree depth (16)
-c max_child - maximum children to index per node (1024)
-r r_limit - max total number of requests to send (100000000)
-p crawl% - node and link crawl probability (100%)
-q hex - repeat probabilistic scan with given seed
-I string - only follow URLs matching 'string'
-X string - exclude URLs matching 'string'
-S string - exclude pages containing 'string'
-D domain - crawl cross-site links to another domain
-B domain - trust, but do not crawl, another domain
-O - do not submit any forms
-P - do not parse HTML, etc, to find new links
Reporting options:
-o dir - write output to specified directory (required)
-J - be less noisy about MIME / charset mismatches
-M - log warnings about mixed content
-E - log all HTTP/1.0 / HTTP/1.1 caching intent mismatches
-U - log all external URLs and e-mails seen
-Q - completely suppress duplicate nodes in reports
-u - be quiet, disable realtime progress stats
Dictionary management options:
-W wordlist - load an alternative wordlist (skipfish.wl)
-L - do not auto-learn new keywords for the site
-V - do not update wordlist based on scan results
-Y - do not fuzz extensions in directory brute-force
-R age - purge words hit more than 'age' scans ago
-T - add new form auto-fill rule
-G max_guess - maximum number of keyword guesses to keep (256)
Performance settings:
-g max_conn - max simultaneous TCP connections, global (50)
-m host_conn - max simultaneous connections, per target IP (10)
-f max_fail - max number of consecutive HTTP errors (100)
-t req_tmout - total request response timeout (20 s)
-w rw_tmout - individual network I/O timeout (10 s)
-i idle_tmout - timeout on idle HTTP connections (10 s)
-s s_limit - response size limit (200000 B)
Send comments and complaints to <lcamtuf@google.com>.
Google Skipfish sample output:

Official website: http://code.google.com/p/skipfish/
Windows binairies download: http://www.shortinfosec.net/2010/03/compiling-latest-skipfish-for-windows.html