OwnCloud looks pretty neat, but I do wish that it would support client-side encryption; I don't trust a machine I'm renting in a data centre any more than I do Facebook or Google. I'm aware that there (sadly) aren't standards for browser-uploaded encrypted files, sharing encrypted files efficiently and so forth, so it's hardly their fault.
If your worry is with data at rest, then owncloud already supports it ( http://doc.owncloud.org/server/7.0/user_manual/files/encrypt... ). I host my servers with AWS so I use Gluster encrypted bricks with backups to a S3 bucket as well as the built-in encryption capability from Owncloud.
Disclaimer: I'm a co-founder of Skylable