How to run strong Go (baduk) playing program locally?
I don't think you're going to get any better free versions. If you purchase a copy of Crazy Stone as mafu suggested it may be stronger. If you like the way those bots play and want an offline version it's probably worth trying it out, as that's the engine that several bots use. However, I say may be stronger because I am not sure that the commercial version is the same as the version run for KGS bots. 

I have no experience with Crazy Stone as GnuGo can still regularly beat me.