After some research for a S3 backup strategy, I settled with s3ql which looks to be one of the most promising solutions for a maintained, compressing, de-duplicating, encrypted, chunked, S3/ssh/sftp based, backup filesystem.

However, the installation of s3ql is non-trivial work because there is no ebuild for it, so I decided to write one. I just pushed the ebuilds to the liucougar overlay on github (which currently contains s3ql and two of its dependencies missing in official gentoo portage tree). As of today, unless you are using testing branch of gentoo, in order to install s3ql, the following lines has to be added to /etc/portage/package.keywords:

sys-fs/s3ql
dev-python/pycryptopp
dev-python/pyliblzma
dev-python/unittest2 #only useful if you intend to test the package
dev-python/apsw
dev-cpp/gccxml
dev-db/sqlite

Please report any issues with github.

Note: if you want the contrib scripts shipped with s3ql installed, contrib use flag should be specified when emerging s3ql.