Here's a few gay characters I noticed. Not sure if they've been posted or not.
Tony from Mother 2/Earthbound is gay, and of course the Magyspies from Mother 3 have no gender. Zangief from Street Fighter, 'dislikes beautiful blonde women'. And well, everything about Cho Aniki. Although in Japan a gay stereotype for men are big muscley bodybuilders...hence the entire premise for Cho Anaki, but still.
Marcus and Dom are definitively bromosexual though.
http://earthboundcentral.com/2008/06/yes-tony-is-gay-and-mr-saturn-is-innocent/