I've read your thread here, and felt like brainstorming a bit.
One of the biggest questions for the villians is "Why now?" My answer is "the internet". (I think
Civilization 4 has it right: the internet is a Wonder of the World.) The kitsune took some time to understand what the humans had built, as they have a fundamentally different way of looking at the world (TV probably was weird too), but with time, they realized that they could use the internet (oddball forums, natch) to organize a global search and destroy mission, familiarize themselves with human tactics and (modern) technology, and research their targets (social networking helping the bad guys getting 'connected'). Maybe all the victims had accounts on a popular world-wide social networking service (you know, like facebook).
Edit:
As for a superweapon, how about something that can overload electronics in an large area. Worldwide. After a couple of demonstrations (Japan and South Korea would be probably ideal), they could hold humanity's technology hostage. As for being a small thing on the galactic scale, it could be a (ham radio equivalent) interstellar transmitter. (If you can cook popcorn and have radiation warnings from a satellite dish...)