I'd say Marluxia. Sora had more reason to hate him then any of the series other villains. That may change once he meets Xehanort in KH3, but for now they don't have any true beef with each other.
^
This would be a great answer if he was in the new organization.
As for me, I'm going with Ansem. He plunged his world into darkness, ripping his home and friends away from him, and almost ruined Riku's relationship with Sora forever. Not to mention, you know, being the asshole that actually started this whole mess. I'm sure Sora is happy that he's helping out as he can, but he never would have had to go on this journey if Ansem hadn't existed and ripped his home away from him. And he almost killed
his girlfriend Kairi as well, so you've got to imagine he doesn't like the guy much.
The most personal Xemnas and Sora really got is when Xemnas strikes Riku straight in the back with the ethereal blades, and other than that he was just a bad guy he had to fight to save the world again.
Again, Swoosh said it best; Marluxia almost destroyed Sora emotionally.
Xigbar... he's just a guy that tells jokes. Sora hates him, but he hates everyone in the organization. He hates Saix a hell of a lot more, I can tell you that much.
Master Xehanort and Sora aren't very personally connected at all. While Master Xehanort is the guy that orchestrated all of this chaos, him and Sora have never really met. The only time they were in the same room is when Sora was asleep; hell, he probably doesn't even know what he looks like! He might have caused everything and almost turned him into a Xehanort, but that doesn't mean it was personal by any means.
And Young Xehanort... Sora fucking HATES this guy. Honestly, he probably hates the young version way more than he'd hate the older version. Young Xehanort screwed with him a ton, I can imagine this being the reason Sora wants to go after Xehanort so bad during Kingdom Hearts III. It's his younger self that pissed him off, not the geezer version we see today.
If I had one choice, though, it'd be Ansem. Sorry, Marluxia, but you were only in one game, so you didn't get to do any further harm.