Today I wrote a patch to Flexbackup 1.2.1 which allows you to define exclude expressions on a per-directory-base (like svn:ignore, cvs_ignore or tar's --exclude-from). Apply this patch and add the following line to your flexbackup.conf:

$exclude_expr_filename = '.flexbackup_exclude';

Flexbackup is a very nice and flexible tool to create full, incremental and differential backups. But if you store your backups in an untrusted environment you might want do encrypt the created archive files. Flexbackup cannot handle it by default, but there is a very simple way to get the desired results by replacing the default gzip binary with a wrapper file.