From what I have read, many of the Elminage games (but not Elminage Gothic) have a marriage option, which allows any two characters to marry and produce offspring (regardless of species and gender).
Also, from what I hear, recent Fire Emblem games have marriage (as does Fire Emblem 4 on the Super Famicom).
Some games have marriage as part of the plot, including Dragon Quest 5, Phantasy Star 3, and Lufia 2. In the first two of those cases, there are choices about who to marry.
A few games have marriages in their endings, like Final Fantasy 4 and Saga Frontier. (The Saga Frontier case is unusual in that the game never explicitely shows who the spouse is, and the most obvious possibility happens to be a same sex marriage--in a game that was originally released in 1997.)
Incidentally, I made a topic some time ago asking about games with same sex marriage:
http://www.gog.com/forum/general/games_with_same_sex_marriage Edit: Regarding Saga Frontier, there are actually two marriages, the one in that ending I described, and one that is a different character's final boss fight. (That game is weird.)