1. Younger Toguro (Yu Yu Hakusho): On the surface, Younger Toguro appears to be a selfish, cold blooded villain who wears sun glasses. However, he is actually an intriguing character with great depth and originality.
Younger Toguro feared one day losing his strength and becoming susceptible to the onslaughts of others. A part of him always craved power as a way of avoiding this from transpiring. However, what truly sealed the deal in him desiring to become powerful were the deaths of his students at the hands of the demon, Kiren. Upon murdering Kiren in the Dark Tournament, Younger Toguro wished to be made into the highest class of demon so that he could obtain unimaginable power and avoid having a situation similar to the one which occurred with his students happen again. However, not too long after his wish was fulfilled, he regretted making it.
Younger Toguro's goal throughout Yu Yu Hakusho is to have Yusuke kill him so he can be sentenced to limbo (the cruelest punishment Spirit World can give) by Koenma for wishing to become a powerful demon. I have never seen a fictional antagonist attempt to accomplish a goal like this before. Usually, antagonists want to dominate or destroy the world, but Younger Toguro sought to be punished for a decision he regretted. Overall, this makes him unique and a nice change of pace from your typical antagonist.
Furthermore, based on what was shown of Younger Toguro in the series, he was a kind and caring man who was willing to go the extra mile for his loved ones. He was also honorable and would give his opponents clean fights without any strings attached.
2. Misato Katsuragi (Neon Genesis Evangelion): Growing up, Misato hated her father, who placed his job above the well beings of both herself and her mother. However, he saved her during the Second Impact. She joined Nerv in order to avenge his death.
After the Second Impact occurred, Misato became mute. It was not until she began attending college that she started to socialize again. Clearly, she is very upfront and bubbly as a way of making up for lost time. Her alcoholism, smoking, flirtatious behavior, and how she leaves her apartment unkempt also stem from her deep rooted psychological issues. Growing up, she desired to be seen as a good girl by the people around her. However, she grew sick of trying to please others. She became wild and rebellious. She also has an Electra Complex. She is attracted to Kaji, who bears a great resemblance to her father. When they were in a relationship with each other in college, Misato fled from him, since she feared the implications that came with this. However, they do rekindle their relationship shortly before his death.
Misato is fascinating from a psychological stand-point. I find her personality and inner conflicts intriguing. Though all of the characters from Evangelion are fun to psychoanalyze, I enjoy examining her character the most. She is a complex person with many layers.
3. Maes Hughes (Fullmetal Alchemist): Hughes rocks. He has two sides to his personality. One side is upbeat and goofy while the other is serious and conscientious. Overall, I feel the two sides of Hughes' persona make him realistic. I know that I have a happy-go-lucky and a no-nonsense side to my personality. Furthermore, he is a nice and friendly guy who is always willing to help others out.
4. Buggy the Clown (One Piece): Buggy is unique. He is a clown pirate. A ******* clown pirate. I have never seen a character like him before. He is also humorous. Additionally, I do not think he is an entirely bad guy. While he may be power hungry and greedy, he befriended the Box Man and his crew was devastated when they thought he was dead.
5. Mousse (Ranma 1/2): I love Mousse. He is an affectionate guy willing to do anything for the one he loves. Some may be put off by his goofy behavior, but I find it endearing. He is not bad to look at, either.