Clint,
You know, it occurred to me after reading your post that I don't have a single writing reference dedicated to creating good villains. I think I'm going to have to remedy that.
The two types of villains I've found to be most successful in RPGs that I've run are either 1) those who are always one step ahead of the PCs and 2) those villains who aside from their villainy seem like almost reasonable people.
I'm also a big advocate of the onion approach. While big villains like cardinal Richelieu can be fun to thwart on a regular basis, I prefer the villains who remain unseen until the end; the mastermind who has been pulling the strings all along, and in a way that, once revealed, makes perfect sense to the players. And, naturally, since the mastermind has been involved from the start, he/she can anticipate all the players regular moves without seeming contrived.
In the WH game I've just started, I've repurposed some of the villains from my old 7th Sea campaign. My players gave me plenty of background fodder from the character questionnaires I gave them, and I'm slowly weaving these adversaries into those where appropriate. I don't want them to be the villains behind every conspiracy, but I want enough connections so that when they are finally revealed, the PCs have plenty of reason to hate them.
Tom