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Step 1
A villain is a necessary foil to the hero. While heroes (those who stand on the side of righteousness and good) are often forced to respond to outside stimuli acting upon them and do not have a lot of latitude in how they respond. But for villains most paths are wide open.
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Step 2
The evil genius villain is different from the mad scientist, in that the mad scientist tends to be amoral rather than evil. An evil genius is generally a clever schemer, while the mad scientist typically pursues scientific knowledge with no regard for the consequences.
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Step 3
Your villain must be fully fleshed out and believable. The villain can often be an everyday person who took a wrong turn, or someone who takes a particular obsession to a new level, who is normal in every other respect, but whose hidden dark aspect would appall anyone who accidentally shone a light on it.
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Step 4
Think about motive. There is something the villain wants, or something he thinks must happen, and he has a belief--sometimes fanatical--about what he thinks is necessary in order to attain this goal. The villains that work the best are the ones where their motive may be basically understandable, but their ultimate goal and their processes are extremely twisted.
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Step 5
A great villain has to have stature and be worthy of defeating; someone who is larger than life.
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Step 6
Developing villains requires the same process as developing other characters. The writer has to ask himself why the villain is behaving this way. It can't just be because he's a villain. He might take something that a normal person would slough off and make it the center of his identity.
