Been trying out various web application vulnerabilities scanners, both Open Source and Proprietary.
These are tools that will analyse your website, or in some case an instrumented copy of your site, and identify some types of common security flaws, or in other cases simple omissions to use best practice.
My main goal is to find tools which are easy to integrate into a Continuous Integration process, so ideally looking for scanners with minimal user interaction, with a command line driven batch mode, to beef up the current CI process.
I've not reached any conclusions yet, but it is an interesting landscape. Almost everyone agrees more tools are better, because they are all slightly different, there are inevitably bugs that one finds, that another misses. CPU time is a LOT cheaper than developer, or Pen Tester time, so a lot of automation makes sense, however the significant false positive rate means that more tools do make some more work. This scales better than I expected, because the same issues trip up different tools in the same way.
For example the WordPress action "wp-post-comments.php" returns a "500 Server Error" HTTP response code under some circumstances, and lots of tools leap on this proudly noting they have "crashed" your server, when the response header shows otherwise.
But alas WordPress defaults to 500 status codes when people omit required fields on forms, and other common cases. This WordPress annoyance has been lurking for at least 4 years, and the Lead Developers seem in no hurry to stop it emitting error codes suggesting it has crashed just because someone forgot to enter their email address.
Almost all the tools pick up on this, and arguably rightly so, but it isn't a useful find.
Intercepting Proxies sit between the browser, and website to test, and thus can easily identify (and modify if needed) any traffic from browser to server. For AJAX, web sockets, and a number of other web technologies this is an essential place to be for spotting certain common vulnerabilities (like failure to validate AJAX server side).
One of our tools of choice is BurpSuite, which is a fantastic little application. You do need to buy the Pro version to do proper automated scanning. Whilst we'll use it for manual, and pre-release testing, its focus is on manual testing, and whilst some folk have tried to drive it from the command line, I suspect down this route lies pain and eternal maintenance.
The OWASP Zed Attack proxy tool is targeted at almost exactly the same space as BurpSuite (Clone?). In true Open Source style it is harder to use, a little rougher around the edges, but allegedly does more, and seems to have a little more momentum and adaptability. Oh and a very responsive lead funded by Mozilla. So far it takes longer to run, and has more false positives, but in my initial tests identify a whole host of minor but legitimate issues, although I rushed it, it still took nearly 4 hours for a small website (CPU time may be cheap but we do want answers before the release date). I suspect many folk who've never used BurpSuite Pro will think ZAP fantastic, and it does look like a little attention to settings will pay dividends in both time to run, and false positive rate.
I suspect either tools can be used in Continuous Integration as a proxy, but I see more effort to support this from the OWASP ZAP lead.
In a previous roles where I was working on PHP and Perl websites, predominantly doing simple forms, the tool of choice was Wapiti. My reading around suggests it is still an excellent choice, scoring well in comparisons and being quick and easy to use. The default version of Wapiti in Debian is 1 until Jessie, so you probably want either a dedicated network security distro like Kali in a machine somewhere, or just Debian testing.
I note also that OSSIM vulnerability scanner (OpenVAS) will run wapiti if it is installed, but again because it is based on Squeeze it is wapiti version 1 you get if you use "apt-get". Still if you need a network security scanner installing OSSIM is a lot easier than installing OpenVAS in Debian, sticking in wapiti is a no-brainer as a one line enhancement. OSSIM can run Nikto with a really minor tweak I've discussed on their forum as well.
Nikto still finds a place in my arsenal. Somehow I can't love w3af. Few of the other tools make me love them (except NMAP of course).
Next on my list are some of the more established proprietary tools, but there are a huge number of Open Source tools I simply won't have time to evaluate, so any tips on where to check first appreciated. I don't see an alternative to the Intercepting proxy, or something logically equivalent, there is also a requirement to handle newer features of browsers like Web Sockets and local storage (which I see as a greatly enriched version of cookie poisoning).
As always these tools won't keep you safe, but they may let you know when you are heading in the wrong direction, which is why using them as early in the development process as possible makes sense.