SQL Injection and XSS are the most common mistakes that programmers make. The good news is that they are easiest to automatically test for, as long as you have the right software. When I am on a pentest I use Sitewatch or Wapiti for finding web application vulnerabilities. Acunetix is over priced.
But, you can't just fire off some automated tool and expect everything to work. There are a number of precautions you must take with ANY vulnerability scanner you choose.
1) make sure display_errors=On in your php.ini Sql Injection tests rely on being able to see mysql error messages in the response pages! No error, no vulnerability detected!
2) Scan the authenticated areas of your application. Create a user account specifically for testing. Acuentix has an easy wizard where you can create a login sequence. If you are using wapiti you can give a cookie to wapiti or give wapiti a post request to fire off but this is kind of tricky.
AFTER you have tested your application then test your server for misconfiguration.
To test your server then you need to run OpenVAS which is the new more free version of Nessus which is now a commercial product. Then you should follow this up with PhpSecInfo. These tests will notify you of problems with your configuration or if you are running old vulnerable software.
Nothing will ever be 100% secure, EVER. No matter what you do there are vulnerabilities that will slip though the cracks. There are vulnerabilities in all development platforms that lead a compromises that no tool can test for. There are also bugs in the testing tools you use. There are false posties and false negatives and some tests that just don't work, a good example i have never seen an automated CSRF tool that actually finds legit vulnerabilities. Acunetix's CSRF test is a complete waste of time.
There is also the OWASP testing guide which goes into greater detail. This is not to be confused with the OWASP Top 10 which is also an excellent resource. The PHP Security Guide is also a great resource for php programmers.
