Here is a "villain" I've played a few variations of as a PC, but which I've always thought would make a better BBEG. The build could vary, but one essential is the ability to steal other peoples' bodies permanently (via Magic Jar + Imprison Possessor, (True) Mindswitch, the homebrew Stranger with the Burning Eyes PrC, etc) plus the ability to either permanently dominate minions (Necrotic Tumor, etc), or to replace their minds with his own (Mindseed). Ur-Priest also fits him well. Here is the most recent backstory I used for him.
Gabriel Lightbringer Jr. was the only son of a Palladin of Pelor, his father, and Anastasia Farseer, a cleric of Pelor. As their only child, he was quite spoiled by his parents. Although he's always been disposed to selfishness and cruelty, his parents had a hard time believing that their son could be "bad". So he found it quite easy to lie to them, trick them, etc, when he needed to cover up some "bad" thing he'd done.
He took his parents' excessive piety, obedience, and charity as weakness, foolishness, and naivety. However, he did learn the value of appearing good to the public eye from them. Their "irrational" faith and altruism was evidence to him that they were completely brain-washed by their church. He has never believed in the "goodness" of Pelor, or any other god. He was always sure that the gods had some selfish motives for wanting more followers, and as an adult he's convinced he's solved that mystery with his discovery of the power inherent in souls, and emotions. Indeed, he is as much an expert on souls as almost anyone, having learned to move his from one host body to another, and to extract the souls of others and sell them, or use them in the construction of magic items, or even... eat them.
Although his parents at times suspected his unsavory nature, as he got older (and became more and more corrupted) he became more and more adept at hiding it. Ultimately, they were convinced that their moral guidance had ultimately prevailed over his inherent selfishness, molding him into a decent and good man. His peers and teachers were not always as easily fooled, but over time any that he couldn't eventually win over have had unfortunate "accidents".
Gabriel was never a physically powerful man, and although what he lacked in physical attributes was more than made up for by his charisma and perceptiveness, he still often coveted those with stronger and more healthy physiques. As he aged and his own body began to fail, he became even more envious, and began researching magical ways with which to strengthen himself. The easiest way seemed to simply steal someone else's body, so he delved into forbidden secrets that allowed him to permanently steal the body of a younger and stronger adventurer (scrolls of Magic Jar + Imprison Possessor, or psionic equivalent). For some time, he kept his own frail body and the adventurer's trapped soul hidden in secret rooms beneath his home, and assumed a new identity. The adventurer was from a distant land, and that coupled with his dangerous occupation assured that no one ever came looking for him.
Although Gabriel is selfish, cruel, greedy, petty, ruthless, and very distrustful of religion, he is a consummate liar, and knows well the value of a good "public face". He has always strived to be a respected member of his community wherever he resides, publicly giving to charities, beggars, attending to his civic duties, making appropriate and often useful suggestions at town meetings and sometimes even holding minor public offices. Although he is almost completely amoral by most peoples' standards, he has always went to great lengths to appear on the surface to be an upstanding citizen and genuinely "nice guy".
In his "dirty dealings", he has always made it a priority to hide his own identity, and make sure there is someone he can easily blame for his crimes: a "second in command" who is actually a "scape goat", whom he himself will implicate when necessary, if the authorities get too close to his "business operations". Thus, his "operations" have always been conducted in secret, and he always maintained disguises when interacting with any of his associates in "unseemly business transactions". Most of the people who have worked for him in these types of things have never even suspected who their true employer was. These "transactions" can and do include every kind of horror imaginable, as long as some profit or personal power can be gained from it. He uses bribe, blackmail, kidnapping, and murder to keep authorities away from his operations, and increase his own wealth and political power.
Of course, things have changed somewhat with the loss of his physical form. Since he no longer has his own physical body, he is basically always "disguised". He maintains a "presence" in different major cities on the prime by enslaving and periodically possessing the heads of a few seemingly unconnected organized crime rings, and spy/assassin networks. He travels around in his raven familiar to "visit" them on occasion when he needs to take care of something himself. His existence isn't even suspected by most members of those organizations, only occasionally whispered about in fear in dark and secret places. Anyone who digs too deeply into these rumors usually quietly disappears.
Not having a physical body has also changed his perspective somewhat. He now looks at things over a longer term, and beyond the scope of the prime material plane, focusing more on the accumulation of immaterial power as opposed to wealth. Wealth can only get you so far. He's thus began "branching out" his operations into other planes, trafficking in souls, with the payments often in services and favors owed to him by devils and powerful political figures on the prime material and other planes.