I think the Disney villains far surpass any of the KH characters, but since the writing doesn't take them seriously in these games, I've left them out.
1.
Ansem’s Apprentice/Terranort ~ I love his design and his voice. He was very eerie in 3D, which might partly be due to his appearance being a constant reminder of what happened to Terra. He's definitely my favorite of all Xehanort's incarnations.
2.
Larxene ~ I love me a good villainess, and Larxene is the only one of the original characters. I don't really care for her antennas, or whatever they are, but I like the mean girl look they gave her. Her sadistic joy at inflicting pain on Namine is extremely creepy. Unlike Xehanort, who does the bad things he does only out of a pursuit of the X blade and/or Kingdom Hearts divorced from emotion, Larxene is emotionally invested in her evil behavior. I also like her fighting style, and her battles were some of my favorites. The voice actress in Re:CoM is a little off from what I imagined, but she isn't too bad (I just thought she spoke waaay....toooo....slooow...)
3.
Vanitas ~ It took me the longest time through the game to realize he was being voiced by Osment (and then the face reveal later). Everything about him I found unsettling at the time. Plus, it was nice to see what Riku's Heartless outfit would like on Sora, if not really Sora.
4.
Saix ~ I really love this character, design, voice, battle, weapon and all. I like how they later revealed his original self was friends with Axel, and how that gives some tragic layers to the character.
5.
Axel ~ I'm not a huge Axel fan, but the character has an awesome design/weapon/voice acting. I rank him here just because he's really effective in CoM, partly because, like Sora, you don't know what the hell is going on. And while we find out later that he was just following orders and/or was in some strange secret alliance with Saix, there's no denying how evil he is in CoM. Killing Vexen and Zexion, both in horrendous ways, imo, justify this ranking if nothing else. Even in KH2, there's still a little bit of that crazy there with how he selfishly tries to kidnap Kairi, not to mention the rapey vibe he gives off in that scene with her on the beach. He's got nothing on Larxene though, who gives off serious child molester vibes.
6.
Xehanort ~ I never really liked this character's design too much. I mean, the clothes are nice (borrowed from the first game), but don't really like the head face/head, etc. He grew on me more in 3D, mostly because the voice acting is probably the best from a non-Disney character. Plus, the way he sits on the throne completely unafraid and speaking "rationally" to Mickey and Riku makes him a total boss. I believe I read somewhere that Nomura based his design somewhat on a primal look similar to a monkey's face? I'm not sure, but either way, that's what he makes me think of. The eyes are the best part. His evil is more disturbing because he really has no personal investment in who he victimizes, he just uses whoever is useful. An amoral evil.
7.
Ansem/Xehanort’s Heartless ~ Billy Zane is incredible and the design is amazing (not to mention hot...). Gets the downgrade just because we later learn he did almost nothing/had very little purpose in the overall plot. But his personality was always bland. Always DARKNESS DARKNESS DARKNESS. Kind of boring after a while.
8.
Riku Replica ~ He really only ranks because the character was so vicious to Sora, and because I thought the Sora-Repliku scenes were the best part of CoM outside than Namine. One of the later battles with him was the hardest in CoM for me.
9.
Marluxia ~ The design is just okay, but I like the scythe and the flower petals. He's a little boring, but something about his one-track-mindedness makes him vaguely off-putting, unlike Xehanort's Heartless who just ends up being annoying. It might be that he's so quiet that I'm left with that impression. Overall, not very memorable in the scheme of things, but he works within the game he's in itself.
10.
Vexen ~ He was one of my favorites from CoM (I know he's unpopular with most fans though). I love his design, although I think his weapon and battles are really bad. The evil he does to Repliku really stands out among other sick things that happenens in CoM. But I think they made a really bad choice of voice actor, who didn't really suit the character at all--at least, I imagined him sounding more bored/cold/condescending rather than Dr. Frankenstein/mad scientist.
11.
Xaldin ~ He gets one of the best deals of the Org. members in KH2, and I liked the character more in his interactions with Roxas in
Days. He comes across like one of the most intelligent members of the Organization, but not as involved. His design is...eh, okay, sideburns. I don't really like the spears, but his battle is easily the most difficult of any of the Organization members in my opinion which gets a few points.
12.
Xigbar ~ Xigbar is another like Xehanort that took a while to grow on me. I like his voice actor and design, plus his more playful side with Sora and Roxas. For whatever reason, he's just never been one of my favorites. It's probably because unlike most of the other Org. members, he knows he's just a pawn to further Xehanort's interests? (Oh, wait, did he know that? I probably have that wrong.) Either way, I hated his original self's design; I only mention his original self because Braig is a villain himself, imo, whereas most of the other Org. members' original selves weren't--or, at least, it's still ambiguous if the other Apprentices knew the evil they were doing, plus we know nothing about some of the others, like Larxene, Marluxia, etc.
13.
Xemnas/Xehanort’s Nobody ~ I've just never liked Xemnas, and I blame that almost completely on the voice actor. Xemnas is like Xehanort's Heartless in that everything's always about NOTHINGNESS NOTHINGNESS NOTHINGNESS all the time. The only real difference is that Billy Zane is awesome, and this guy's voice actor is not. He's okay in small doses, like in 3D, but definitely not as a main villain.
14.
Zexion ~ These last 4 I only rank because they are in the Organization and attempt to kill either Sora or Riku. I like Zexion the best of those left, so that's why I rank him first. I love his design and his voice actor--who would've guessed Darien would've ended up in
Kingdom Hearts?!
I like the mystery of his weapon and he seems like the next intelligent in the Organization to Xaldin (to me), too.
15.
Luxord ~ Like Zexion, he's only interesting because of his powers. His design is bland to me and he doesn't really leave any impression.
16.
Demyx ~ I actually like Demyx as a character, but not as a villain. I normally like water-based villains, but not here. Using a sitar to fight is a little bizarre, and not in an interesting way.
17.
Lexaeus ~ Dullsville.
This is just ranking their Nobody selves before they were restored. At first, I wasn't sure if I should add Axel or not. He's more of a grey character, since he does some bad things in CoM, but doesn't seem aligned with the others either.
