A great trick is the red herring reveal. Your villain is
1: someone using a pseudonym while their actions are plotted
AND
2: That person is also someone close enough to the heroes that they know them and their backgrounds but would never consider them as the villain until the final reveal - when all the little hints and comments come together.
This has been done in a couple Bond films and Suzanne Chazin uses it in Flashover. I won't spoil it for anyone, but the villain has be be one of the best I've read in years.
(This also works as part of a 'Ten Little Indians' plot - if the prime suspect is dead, who is the villain?)
