This document details how I setup LE on my server. Firstly, install the client as described on http://letsencrypt.readthedocs.org/en/latest/using.html and make sure you can execute it. I put it in /root/letsencrypt.
As it is not possible to change the ports used for the standalone authenticator and I already have a nginx running on port 80/443, I opted to use the webroot method for each of my domains (note that LE does not issue wildcard certificates by design, so you probably want to get a cert for www.example.com and example.com).
For this, I placed config files into etc/letsencrypt/configs, named after <domain>.conf. The files are simple: