You'd think that after 4 years on here I'd get around to actually writing something...
HP: remus/tonks, lucius/lily, lucius/narcissa, bellatrix/rodolphus, snape/anybody really lol- not too picky when it concerns him!
FF(all): squall/rinoa, rikku/auron, ashe/basch, fran/balthier
LotR: aragorn/arwen, faramir/eowyn, boromir/OC
Star Ocean: maria/albel (totally non-canon and i don't care!), cliff/nel, mirage/adray
Ghost in the Shell: batou/motoko (who else is there really?)