If we don´t count what happens post NJO I would say Jacen/Tenel Ka, afterwards it becomes kinda dodgy. Like with Tenel more or less forcing him to sleep with her at one point and her whole wanting to have her cake(a child with Jacen) and eat it too(not marry/aknowledge him to not offend the Hapan nobles), as well as how readily she abbandons him in LotF without makeing at least an honest attempt to redeem/reach out to him really sour the whole relationship. On some others I found Raynar/Lusa always pretty cute, and just hate how they destroyed that in NJO, Lusa dying offscreen Raynar makeing out with a one of character in that same book like a day after learning of her death. Also Obi Wan/Siri, wich is yet another pairing I like that later SW works have kinda destroyed, when they brought Satine into the mix. If we include rpg/fanfic I would also add Adrian Malek/Marie Firestone, at this point probably my OTP. Hm, probably less than most people, actually grown quite apprechiative of stories without a pairing in recent times. Some I tend to ship are: Shepard/Samara(Mass Effect), Garviel Loken/Mersadie Oliton(Horus Heresy), Tullus/Sirona(War of the Eagles), Arkhan the Black/Queen Neferata(Warhammer/Age of Sigmar), Haleth/Caranthir(Silmarillion), Eskel/Triss(The Witcher). Not really into that though if I had to pick one Illidan/Maiev(Warcaft) which actually has some hints for it, even if it would be rather unlikley. Also Daala/Isolder from one alternate universe rpg I once played with friends. Ben/Vestara would be one in SW, because it would be based on utter hypocrisy. Generally not fond of hero/villian pairings, these can be done well but sadly often boil down to "the villian is mainly redeemed/left of the hook because the hero wants to have sex with them".