I'm not sure if I understand you right, but look into the configuration file:
//Set target to use when creating links - leave empty for same window
$conf['target']['wiki'] = '';
$conf['target']['interwiki'] = '';
$conf['target']['extern'] = '';
$conf['target']['media'] = '';
$conf['target']['windows'] = '';
Doesn't that fit to your problem?
So my configuration looks like:
$conf['target']['interwiki'] = '_blank';
$conf['target']['extern'] = '_blank';
Ciao
BlackFog