Originally Posted by Steve M

My understanding is that much like arriving US Immigration, foreign nationals that have permanent residency in Japan (that is, gaijin card with re-entry permit) are allowed to use the Japanese National lines. All others are to use the Visitors line without respect to who they're with. Well, actually there's a third line at some airports for sangokujin (aka "special permanent residents") but you'd probably already know if this applied to you.