Xemnas - Love his FM secret boss battle and his Final Form fight in KH2. When Nobodies were actually Nobodies and had no confirmation of hearts, I loved how he was the only one to ever act emotionless - Paul St. Peter does an amazing job voicing this character. I love his dramatic sweeping gestures and how even his laugh sounds void of anything. When he told Sora he unfortunately couldn't remember anything other than the emotions of hate, rage, ect. it honestly made me feel a little bad for him. It felt like his past life must have left him in a dark place - which I assumed came from Terra after playing BBS. His character has changed since DDD, but even then his boss battle was awesome, and thus I still like the character.
Roxas - I don't like Roxas as much as I like Sora, but I like him all the same. His boss fight in KH2FM is awesome, and I like how he always seems to be fighting for some respect: hates being kept in the dark, hates being treated like a pawn, ect.
Axel - While I've never cared for Lea, Axel was a boss in CoM. I loved his deviant nature and even liked his arc in KH2. As for Lea, I felt he got way to much importance added onto his character in DDD. Axel excelled in his role as a supporting character, and I would have enjoyed Lea much more if he had stuck to that role.
Marluxia - Pink is, without doubt, incredibly manly - even if his hair was brown in the original. Lord of the Castle, Scythe of Pedals, and Graceful Assassin are by far some of my most favorite pieces from Kingdom Hearts and I loved every stage of Marluxia's boss battle in ReCoM. He was a sophisticated and ambitious prick, and I was ok with that.
Xigbar - I don't know what to say about this character. He seems like a pretty interesting guy, but I don't know what the hell he's after, or if he's even after anything at all. He has to be, right? He's willingly - at least, that's what it seems like - been with Xehanort since the start, but has never given any clarity as to why. His quotes during his boss battle always make me smile, though: "Look what I saved for ya!", "I lost? ME?".
Sai'x - He's sort of like Xigbar for me. What exactly makes him act the way he does? What happened to make him so loyal to Xehanort, if he even is. Like Xigbar, he also has awesome boss battle quotes.
Luxord - The way he acts like he's always one step ahead of his opponent is something I've always liked. His reaction command at the end of his boss battle made Sora look like a badass, and I'm okay with that. Wish he would have had more screen time, though.
Vexen - Fighting his KH2FM variation with Stitch as my partner makes him by far one of the best battles in the game for me. If you haven't tried it, give it a shot. I also enjoy taking him on without any sleights in ReCoM. Other than his boss battles though, I never really cared for his character. He only served to boost Axel's awesomeness for me when was killed. Even seemed pretty cool, though. I like how he had enough insight to immediately tell what Ven was by just looking at him.
Demyx - I hated this boss until I remembered that Thunder was my friend. I liked his goofy nature, and how at the same time - once Sora pushed him to it - he had no trouble showing his emotionless side. "Silence, traitor," is oddly one of my favorite lines. But, despite my likes, he didn't really do much of anything.
Larxene - A total bitch. While I don't dislike that in a character, I wish she would have shown at least one other personality trait to me. Her boss battles were always fun and challenging though.
Xaldin - Never understood his infatuation for Beast. I say infatuation because his taunts and actions towards him seemed like personal vendettas. I may be thinking overthinking it and he may have just been trying to get his Heartless and Nobody, but still, he enjoyed it too much for my taste. It was almost like Beast represented something in his past for him, but most of the organization members don't have fleshed out back stories, so I can't really tell. Despite, he was the first and only boss to get me to summon King Mickey during my first play-through of the game. He also wields one of my favorite elements.
Lexeuas - The strong, silent type who apparently had morals... that he didn't have enough screen time to show. I did enjoy his battle in KH2FM.
Zexion - Didn't care too much for this character. I didn't hate him, but I didn't like him either.