I would like to integrate vulnerability scanner as part of our build process. Are there any open source tools worth looking at?
Perhaps your first step should be: Nikto
Incidentally this is probably better directed to ServerFault than here at SO ... it's more relevant to sysadmin than programming.
The best open source scanner for web applications is Wapiti. You will get a low false positive rate and good site coverage.
There is also w3af which is tests for more types of vulnerabilities than wapiti, however its more error prone and the "WebSpider" discovery modules isn't very good.
If your site is ajax heavy you'll have to go with a commercial product like Acunetix or NTOSpider.
Make sure that error reporting is enabled during testing and disabled during production.
Take a look at this list:
WASC - Web application security scanner list
There are plenty of open source and free web app scanners in there.
Also not open source but free:
- Acunetix Free : http://www.acunetix.com/cross-site-scripting/scanner.htm
- Netsparker Community Edition : http://www.mavitunasecurity.com/communityedition/