HackerTarget.com provides free security scans for websites. You can purchase a Scan Membership, which then removes the scan limits per day.
They provide scans using known, Open Source tools, including:
* Nmap Port Scan
* Nikto Web Scan
* OpenVas Scan
* SQL Injection Test
* BlindElephant Scan
* WhatWeb Scan
* WordPress Scan
* Drupal Security Scan
* Joomla Security Scan
* SSL Check
* Domain Profiler Report
* Server Info