CLAMP have a way of creating couples that you absolutely want to root for, so it's a little difficult to just pick one, but my favourites are Sakura and Syaoran (both in CCS and Tsubasa), mainly because of the sentimental value thing (for me)- they're adorable in CCS and so cute that I want to glomp them, while Tsubasa is the 'older' take on them (though of course, by now we know Tsubasa's Sakura and Syaoran aren't really the CCS pair). I love that we get to see them two ways, from cute and fluffy to tortured and angsty (words I'd never have associated with those two in CCS)- same souls or not, I will always ship them.
Re: Subaru and Seishirou, I so wanted them to meet in the Tokyo Revelations arc of TRC, but sadly that didn't happen.