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There are many concerns about backing up servers (naturally), and the best responses I found for "backing up best practices" was http://serverfault.com/questions/512/best-practices-to-keep-your-computers-backed-up-efficiently/1076#1076.

However,

Many people recommended 'rsync', but there are many rsync applications out there (like rsync-backup and duplicity, etc), and I want to know the trade-offs and recommendations for which one to use. Is there one that simply is newer and technically superior to all the rest?

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I've used many of them ("vanilla" rsync, rsnapshot, rdiff-backup, and duplicity), and I've found duplicity to be superior to all the rest. Its ability to deal gracefully with incremental, encrypted backups isn't found anywhere else in this class of backup apps. Also, it's quite flexible as far as what back end storage it uses. I use Amazon S3 with duplicity, but it can all use scp, ftp, dav, etc.

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