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yeah, it can be a pain. one thing I do to make the db much smaller is kill all of that stupid incoming links and news and new plugins bullshit that appears in the admin panel. all of that inexplicably gets cached in the db and takes up huge amounts of space.
unfortunately, the only way i've figured out to kill it is to edit the wp-admin/includes/dashboard.php file and comment out the wp_add_dashboard_widget calls for those things: dashboard_incoming_links, dashboard_plugins, dashboard_primary, and dashboard_secondary