Sure, I can encrypt the file on my computer, store it over there, transfer it to my other computer and then decrypt it. That is, of course, very inconvenient. What I really want is something which will sync the files. Between two machines that is not really difficult but I want a generic solution where over there can be some machine I don't have total control over.

Rather that try to re-define the problem, take a look at http://owncloud.org/index.php/Encrypted_File_Storage_Proposal_II . It does a good job of defining the problem and at least proposing a solution. It helped me get on track with how this is not exactly trivial.

If you have a working solution that addresses everything in owncloud page, let's talk.