Kane and Revolver Ocelot (which now is partially Liquid so Liquid Ocelot or whatever Kojima calls it). Kane because he's Kane, one of the few villains that was smart to use a thing like the media over just guns: "He who controls the media, controls the world" it just says everything.
And Revolver Ocelot, he betrays everyone! He triple crossed the russians, backstabed the americans, Liquid and even the Patriots! I'll enjoy his death on MGS4 greatly.