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Typically you're going to want to at least back up /home. If you're running a web server the you may want to include /var/www (or whatever your webroot is). If you're running databases, you'll have to lookup the best way to back those up for whichever type you're using. It's also usually a good idea to backup /etc/passwd and /etc/group. If you're running a bunch of services and you have plenty of backup space, you may just want to backup all of /etc since there are lots of configs in there. Leave /var/log, /tmp and /dev alone.
/Sys has a psuedo filesystem, so you don't back it up.
lost&found should be empty. It is were orphaned files found during fsck are copied to.
There may be links in the users' home directories to directories in /tmp. Make sure that you backup symlinks as links, instead of following the links and backing up the files.
If you use tar, you may find the -g <timestamp> option useful. It backs up files created or changed since the last backup.