It would take too long to name all of my favorites... Because honestly, who can choose just one? So, I'll limit myself to CLAMP creations. Then again... I'll take almost all cannon pairings in a very loosely-defined soulmate capacity... Special mentions do go to Amaterasu and Souma (Because CLAMP doesn't exactly put out non-tragic lesbian pairings every day... I'll take what I can get), Touya and Yukito (Tsubasa made it pretty clear that they cannot exist without one another, not to mention that they actually exhibit healthy relationship practices), Kokuyo and Hisui (The ultimate elopement), and Fujimoto with Kobato (The eventual May December Romance bit is a little weird, but it still ends up resolving the plot nicely). One notable exception to canon is Hokuto and the Gaijin Girl. There were no happy campers the day that ship sank. That whole ship was choc full of interesting social and political commentary, and then... Nothing. We never find out whether the Girl was deported, whether Hokuto said goodbye before her Ultimate Plan... Ugh.
<crying>
I just have a lot of feelings...