My top 3:
1.-GMK Godzilla: Why? Because this guy is supposed to be a freaking demon! And it's almost like those white eyes have EVIL POSSESSED KAIJU written all over them.
2.-1984 Godzilla: It's just jaw dropping to see how much damage this guy can do. The result of the JSDF fight against this Godzilla did not end in utter defeat, but in a massacre.
3.-1991 Godzilla (After the timeline is altered): This guy doesn't just come even stronger than before, but also proceeds to anihilate everything in his path: The JSDF, King Ghidorah and Mecha King Ghidorah.
I wouldn't coun't Gojira (1954) as "EVIL", he's just indifferent towards humans, it is like if you put a random guy (protected with a Hazmat suit) inside of an ant colony, the dude is just going to make his way through the colony and he's going to completely destroy the place and crush hundreds, if not thousands, of ants in the process while these try to put some futile resistance.
In my opinion an "indifferent" Godzilla is scarier than an "evil" one. With an evil Godzilla you actually know that he cares about humans because his sole purpose is to destroy them (like GMK Godzilla whose sole purpose was to destroy Japan). A Godzilla with an "indifferent" attitude is worse because he just won't give a **** about humans, he just makes his way through the city crushing stuff and killing people (while not being his main purpose) and if someone provokes him (when the army tries to defend the city) then things get more ugly.