Xemnas
-He strayed from the original plan and became corrupt. He wanted to become not only complete, but a godlike being who would reshape the worlds the way he saw fit. He had to be stopped.
Xigbar
-He was just following orders it seems. Though he was responsible for turning the Dragon into a heartless, in the end no one got hurt.
Xaldin
-Another one who I believe was just following orders. Th only evil thing he did was to kidnap Belle and manipulate the Beast. And he did it in such a cool evil way.
Vexen
-He actually wanted to help Sora, but in the end was cut down by Axel. He seemed like one of the few members who wouldn't stoop so low just to get their hearts back.
Lexaeus
-He wanted the Organization to stay the way they were, and wouldn't let some new comers take over. I don't think he ever realized Xemnas' true plan.
Zexion
-The one who started everything. It was he who insisted Ansem the Wise to continue research of the heart and it was he who helped Xehanort with his plans. The way he manipulated people made him even less of a character worthy of living.
Saix
-My personal favorite member. He seemed like the smartest of all the members, as well as the most evil. He truly knew what was going on, and was Xemnas' right hand man. In the end he redeemed himself for his evil deeds though, when he pleaded to Kingom Hearts that he only wanted a heart.
Axel
-I don't think he cared for his heart, or the Organization's plans. All he wanted was to be with his friend and if that mean't backstabbing and betraying the Organization while lying to others, he would do it. Its a good thing he didn't die by Sora's blade.
Demyx
-I think he was just following orders. He seemed oblivious to the Organization's true intentions and only wanted his heart back. I didn't like that Sora had to go and kill him rather than letting him go free, he might've changed his ways . . .
Luxord
-Another member who was following orders and acting on behalf of the Organization. He never truly did anything too evil and no one got hurt, he only fooled around in Port Royal while looking for something "worthy of serving Organization XIII." His death could've been avoided.
Marluxia
-I think the reason he betrayed Org. XII was because he saw it had become corrupt. The way he used Sora and Namine though, made him seem more evil than what his intentions were.
Larxene
-Same as Marluxia.
Roxas
-Never died, but never deserved to be manipulated and lied to like he was. He was a lost confused Nobody who was only searching for the answers to questions he had about his past. I'm glad that he ended up with Namine, after all the crap he had to put up with.