encfs is a super simple option. Setup is easy, and all you have to do to mount the encrypted folder is:
encfs $ENCRYPTED_DIR $MOUNT_POINT
I like to create a directory and remove all read permissions and use it as the mount point, and a hidden directory for the encrypted file storage. Mounting the directory turns the permissions back to normal, so I can only write files into the folder if it's mounted, keeping me from accidentally adding files to the mount point that won't get encrypted.
On solution I was looking at was using EncFS and then Google Drive or Dropbox to backup the encrypted drive. The nice thing about EncFS is it keeps your encrypted files as individual files, so every time to change a file you don't have to sync the whole drive with the cloud.
EncFS. I wont use software that was taken down in such a strange way as TrueCrypt was.
Website: http://www.arg0.net/#!encfs/c1awt Windows Port: http://members.ferrara.linux.it/freddy77/encfs.html Introductive Tutorial: http://sdf.org/?tutorials/encfs_tutorial
Yeah I can't really rely in CLI tools for standard users (but it shouldn't be too hard to quickly write a GUI for it), not only that but I was really after a filesystem-level solution.
The one tool I've found that is easy to set up encfs that has a Windows port had an audit written up on it and it's basically shit. If someone wants to break it they can use build-in Windows backdoors to take a few snapshops of the encrypted filesystem and use that to break it.
I'm not going to recommend an open source tool that hasn't been audited properly with very positive results, and for now that just doesn't seem to exist.
You haven't mentioned your OS. Why not use rsync itself? If you are on *nix then you are all set. Or you can use cygwin. I first dump everything to an encrypted volume in linux. After mounting the encfs volume:
sudo /usr/bin/rsync -rlpt --delete --delete-excluded --exclude-from=/home/me/filesNotTobackup /home/me /d1/enc4dhmount/home/
Then, rsync the resulting encrypted filesystem itself to an offsite location:
/usr/bin/rsync -e ssh -rlptz --progress --delete --delete-excluded --exclude '.encfs5' /d1/enc4dh-raw/ me@remotemachine:backup_me/machinename/
That's actually pretty awesome. On the other hand, I wonder if it wouldn't be sufficient to use something like encfs on the client. Still, it's helpful that you have this as a goal.