I share the sentiments of most other posters what makes a bad villain motivation- 'evil just because, gonna blow up or take over the world 'cause I was mistreated as a kid'. Not that it necessarily makes a villain bad, just shallower than some. There is a certain majesty to facing a legendary evil such as Ganondorf or Dracula that lets you excuse them.
As for the rest however, two motivations stand out as interesting in my memory. Janus Cascade in Wild Arms 3 starts out frantically trying to pay back some kind of debt to a far greater evil (not unlike Dr. Facilier in Princess and the Frog if anyone liked that, a debt to the devil is a powerful yet semi-sympathetic motivator), but eventually that debt does get called in and he ends up an unwilling servant to the main baddies. Emphasis on unwilling- when he can get away with it he gives you hints and helps you to banish one of their other extremely powerful servants. However, the true core of it goes all the way back to the kind of notorious bandit he originally appeared as- he actually wants to pull a crime so infamous that everyone will remember his name forever (a crime to top all crimes, a crime that will live in infamy!... sorry). As he admits, he doesn't believe in the afterlife, so this is the closest thing to immortality he can find.
Secondly Elpizo from Mega Man Zero 2. While without context he might seem like nothing more than a retread of Sigma from the X series, he's lived and grown up in a different age where Reploids, his people, are second-class citizens, easily declared Maverick due to an energy crisis and terminated. He is one of those ones who starts out with pure motivations, even becoming the leader of the rebel group you are in, but gradually becomes corrupted by his resentment of humans, resorting to progressively more and more ruthless means to get the power to make his goals come true, such as sacrificing his own troops. Certainly the most sympathetic Mega Man villain ever.