Multiple keyword-specific domains pointing to our VPS IP

We are having some issues with not showing up (at all) in Google SERP for specific keywords (potentially our most effective keywords) and have just noticed that there are a number of keyword-specific domains pointing to our VPS IP. These domains are using the keywords for which we are not ranking (as if completely invisible). For example propertyforsalelondon.com, propertyforsalenewyork.com, and so on. I am aware that Google frown upon having multiple domains (especially keyword-specific domains) pointing to the same site. In fact these domains are showing up in Google SERP with all of our content (title, keywords, description, etc.) - being that they are just domain aliases. Could you advise on the correct method for blocking these domain aliases from our VPS? I'm not concerned about a redirect, I want a full and complete denial for any domain that is not ours (obviously still allowing crawlers and robots to access the content). I did previously set up a named vhost for a specific domain and configured deny,allow; deny from all - but it looks as though this was overwritten when our new SSL cert got installed??