You could use something like Cloudfogger to encrypt the cloud-based copies of your files. There are several other products, some which only support Dropbox. You could also choose a cloud provider that, say, doesn't store your data within the US, or which uses its own encryption driver using keys you generate, such as Mega (though that's got problems with speed).
Alternatively, you could set up your own VPN using something like NeoRouter, then sync machines across that using any of a number of tools such as AllwaySync or the OS' own sync tools.
As with all these things, the more you secure your data, the less useful some of the social tools become