1. Romance. Villains frequently have ulterior motives (like marrying Aunt May to steal the nuclear power plant she inherited?) and improper means (such as sabotaging rivals). True romances are rare for villains and can make them deeper and more interesting. Mr. Freeze’s romance with his wife Nora in Heart of Ice turned him from a corny ice-themed punchline into an Emmy winner. (He later devolved into a corny ice-themed punchline after being played by Arnold Schwarzenegger, but some things can’t be helped).
2. Revenge. This might be heroic if the crime is particularly heinous and/or the regular authorities are not willing or able to resolve the situation. It might be villainous if the character is overreacting or not being careful enough about hitting only the people responsible. When working with revenge plots, I think it’s usually more interesting if the revenge develops into something more than just killing/stopping people A, B and C. For example, in Scott Pilgrim Vs. the World, the villain is getting back at the love interest that rejected him, which introduces relationship issues that present their own challenges to a protagonist trying to get over a long-dead relationship of his own.
3. To distinguish oneself. It depends on why the character wants to distinguish himself. A hero whose main goal is fame/status will probably gain a more substantial goal over the course of the story. (For example, Booster Gold). I think it’s seen as a superficial, temporary goal. In contrast, “be true to yourself” is more purely heroic… Unless being true to yourself involves psychically decapitating people and sucking out their brains.
4. To fit in/gain acceptance. A lot of heroes seek to gain the respect of their peers (see any story about “the new guy,” particularly students). However, gaining acceptance might be more sinister based on who the protagonist wants to impress and/or what will impress them. For example, 1984 ends with Winston Smith rather unhappily gaining acceptance by betraying his innocent girlfriend: “…he had won the victory over himself. He loved Big Brother.”
5. Justice. This is like revenge, but usually less lethal and targeted more carefully against the perpetrators. Nonetheless, justice can sometimes be villainous. For example, the main goal of the robot antagonists in the I, Robot movie is to prevent humans from getting hurt, and they think that putting human under house arrest is the most logical way to do so.
6. Greed. Although realistic, I think this motivation tends to be used in a one-dimensional way. For a bit more depth, maybe the character is hoarding something (money, power, remote-control ninja stars) on behalf of somebody else. Also, I think it’s cliche for antiheroes to be sort of greedy because their authors are afraid to let them do anything actually unpleasant. I’d recommend going all the way.
7. Fear. This strikes me as a more interesting, dramatic motivation than greed. It’s usually more morally complex because the character might actually be right. Maybe Lex Luthor is correct that Superman will eventually turn on us. Fearful heroes usually perceive threats that are current rather than potential, but they may be paranoid wrecks anyway (see Question/Rorschach, possibly the psychiatrist from Halloween and Batman, etc).
8. Desperation. I feel this is a more interesting motivation for both antagonists and protagonists than greed because it raises the stakes and heightens the conflict. A greedy character is usually driven by stupidity: stupidity is the only reason he can’t be satisfied with what he has. In contrast, a desperate character can’t back away from the plot. He can’t escape the conflict.
9. Social cohesion. Most commonly, this means keeping a family together. However, any books with significant racial or class-based conflict probably deal with this to some extent. Some examples: X-Men, probably Harry Potter, American Beauty, The Incredibles, Dark Cloud Descending, etc.
10. A desire to better oneself. Depending on what the character is trying to change about himself, we may approve of the transformation. Here’s a thought for your hero: is he trying to change anything about himself besides becoming more powerful? What about the villain? This could play out in a more sinister way if the character’s desire for self-improvement or self-advancement gets other people hurt. (For example, it’d be really shady for a police officer to put down a case just because pursuing the case could harm his career).
11. A desire to better humanity and/or society. I find altruistic villains especially fresh. They’re harder to dismiss as stereotypically evil, cardboard cutouts.
12. Curiosity/search for knowledge. A hero searching for understanding may be an amnesiac, some sort of wanderer, etc. A villain is probably uncovering secrets better left untouched, although his intentions may have been pure. More unexpectedly, an eventual villain might go on an innocuous search for understanding but come away with exactly the wrong lessons from life. If starting point A is a relatively normal person and ending point C is a villain that kicks dogs without any hesitation, the journey is what connects the two points. What sort of life experiences would warp someone that much? (See The Heart of Darkness, for example).
13. A desire to gain power to achieve a goal. This training/self-development angle comes up in many superhero stories, particularly those with rookie protagonists (such as Kickass). However, it was notably missing from Scott Pilgrim vs. the World.
Could I recommend against a stereotypically heroic goal for the heroes or a stereotypically villainous goal for the villains? While world domination is a fine feat, it is not exactly uncharted territory for supervillains. If the villain is vying for world domination, why? It might be more interesting if his bid for supremacy is somehow tied to altruism, fear or desperation. For example, maybe the villain is a time-traveler that knows about some grave threat, so he’s trying to take over because he’s the only one that knows how to avert disaster. If the alien invasion starts in 20 years, you don’t have very much time to unite the Earth. (Also, this would lend itself rather well to a sequel: the hero successfully stops the “villain” at the end of the book, but discovers that he has to defeat the impending alien invasion).
14. To escape one’s destiny. This comes up quite a lot in classic American literature, such as The Grapes of Wrath, Catch-22 and The Great Gatsby. In contemporary superhero stories, the element of fighting destiny comes up most often when a character decides to become a superhero. Very few superheroes are born into their line of work. What leads the protagonists to decide that this is their calling? A supervillain rebelling against destiny, such as Sylar or the Kingpin, is usually born into a decidedly mundane and powerless family. Another common type of escaping destiny is fighting with one’s parents and/or dealing with stereotypes.
15. To achieve one’s destiny. The favored goal of Chosen Ones and megalomaniacs everywhere. I don’t think this is nearly as interesting as escaping destiny because a destined hero isn’t really driving his own story so much as conducting a train on a track laid by somebody else. If I had to shroud a character in destiny, I’d rather make it the villain The Boy That Lived, The Chosen One, the child born under a rare astrological sign, the subject of a great prophecy, the heir to an ancient and illustrious organization, etc. It’ll make the hero’s journey all the more challenging if he has to overcome all that on his own.