From the first moment I heard about Let's Encrypt I liked it and wanted to use it as fast as possible. But the more I read how they want to implement it, the more I dislike it.
Current project with automatic configuration is not what I want to use at all. I have many very complicated configs and I do not trust such tools enough to use them. I like UNIX's single purpose principle, tools should do one thing and do it well – nothing more.
But there is one neet tool that use Let's Encrypt API only leaving all configuration for me, it's acme-tiny python based script. I won’t copy/paste examples – documentation is written pretty well.