The only pair I ship is Sora and Riku. It's not even about shipping, though I find them adorable. For me, their relationship is so interwoven into the narrative, that at this point I can't separate the two. It's why I have little doubt that they are intended endgame.
Beyond that, I think Lea/Isa, and Roxas/Xion are cute. Namine and RR is also interesting. I wish we could have seen more between them. I think that it would be poetic if they were able to form some genuine, happy, memories, together, that were based on mutual affection rather than a scheme.