Full disclosure - I had not heard of this being done before, and had not really even considered it. I do use alternate DNS servers on our home PCs for various reasons (speed, malware blocking), but implementing an encrypted connection to the DNS server was not even on my radar. The good people at HowToGeek have come up with a guide to doing just that, though.
DNSCrypt, from the great team at OpenDNS, is the simple solution that we’ll use to add encryption between your computer and the DNS server. It’s a lightweight solution that works on either Windows or Mac — sadly no mobile support so far.
What this tool is actually doing is creating an encrypted connection to any of the supported DNS servers, and then creating a local DNS proxy on your PC. So when you try to open howtogeek.com, your browser will send a regular DNS query to the 127.0.0.1 localhost address on port 53, and that request will then be forwarded through the encrypted connection to the DNS server.HowToGeek