Is there an automated tool that takes a list of hosts and figures out which common web applications (such as Wordpress, Mediawiki, Joomla etc) they are running and - if possible - which version and which plugins are installed?
In addition to Whatweb that @tate mentioned, there's a couple of other options that I'm aware of/use
wpscan is targeted at wordpress and can discover version and installed plugins. It also reports potential vulnerabilities in discovered plugins, but from what I can see that's just based on the plugin being installed, not specifically the version being vulnerable.
Nikto is still a good choice, in my opinion, as it's database has been built up over a number of years and it does a decent job at identifying a variety of installed software
There are plenty of cloud-based scanning tools and plugins that can help. Here is a list of all the free ones: 1. Qualys 2. Scan My Server 3. Sucuri 4. Web Inspector 5. Acunetix 6. UpGuard 7. Tinfoil