Great thing happen securing internet servers, And it's Free.
But there is catch, You have to renew your certificated Often.
Since they provided tool to do so, i don't think there is problem at all.

First install command line API tool. letsencrypt source

There is many way you can get new certificate or renew certificate.
But i like following way, which can be scripted easily.

Get New Certificate

./letsencrypt-auto --email <email> --agree-tos certonly -d <fqdn> -c <Location_for_config>

It is good idea to create config file for each certificate because we can use it for renewal

sample_config

# Domain which you are trying to get certificate for;
domains = wiki.k2patel.in
 
# Define rsa keysize
rsa-key-size = 4096
 
# Define the api server
server = https://acme-v01.api.letsencrypt.org/directory
 
# email address for your certificate
email = k2patel@rediffmail.com
 
# we can disable the UI and turn on the text mode
text = True
 
# authenticate by placing file in webroot located under .well-known/acme-challenge/
authenticator = webroot
webroot-path = /var/www/letsencrypt/