How to transfer multiple databases by sql-sync?
Drush sql-sync will only copy one database per run; if you have multiple databases to copy, you must run sql-sync multiple times.  Use --source-database=other and --target-database=other to specify some other database.  Use --source-target=mirror and --target-target=mirror if you want to copy a secondary mirror of your Drupal database (not your use-case).

Rename 'other' and 'mirror' to match the appropriate key of your database record.  See figure below.

Array
(
    [default] =&gt; Array
        (
            [default] =&gt; Array
                (
                    [driver] =&gt; mysql
                    [username] =&gt; www-data
                    [host] =&gt; localhost
                    [database] =&gt; drupaldb
                )
            [mirror] =&gt; Array
                (
                    [driver] =&gt; mysql
                    [username] =&gt; www-data
                    [host] =&gt; localhost
                    [database] =&gt; mirrordrupaldb
                )

        )
    [other] =&gt; Array
        (
            [default] =&gt; Array
                (
                    [driver] =&gt; mysql
                    [username] =&gt; www-data
                    [host] =&gt; localhost
                    [database] =&gt; otherdb
                )

        )

)


Update from NenadP:

It seems that you need to add --strict=0 when using Drush 5 to work around a bug in the sql-sync command definition.  This has been fixed in Drush 8.6-6.x.