The CIA Sets Up Shop on Tor, the Anonymous Internet
wired.com
wired.com
* Onions are more secure as they do not rely on x509/certificate authorities and DNS
* Visitor privacy
* Ability to research the traffic going to their site. They could probably learn patterns from it.
Also, in recent years onions have become also appropriate for "clearnet" sites. There is a config option for Tor to disable server-side privacy, keeping the visitors anonymous but speeding up the connection by reducing the server's hops.