Well if we are going to point out our personal flaws with this list (I kind of see it as fans vs. general population), my comments would be as follows:
Godzilla
GMK
Godzilla Against Mechagodzilla -
This is an entertaining movie, but it is way to high.
Godzilla vs Destroyah -
Aside from Godzilla's death, this movie is nothing but beam wars and bulky suits. Godzilla's death and the throwbacks don't redeem it, still too high.
Godzilla: Tokyo SOS -
Similar sentiment as Godzilla Against Mechagodzilla, but I actually prefer it over Godzilla Against Mechagodzilla.
Godzilla Final Wars -
This movie is waaay to high, especially based on the movies it's passing. It sort of supports my personal generalization theory that a lot of non-hardcore fans / casual viewers enjoy this movie since it re-enforces Godzilla stereotypes.
Ghidorah, the Three Headed Monster -
I can't believe a Golden Age movie is being snubbed for modern films.
Mothra vs Godzilla -
This is inexcusable. Mothra vs Godzilla is one of, if not the classic Godzilla movie (Along with KOTM and King Kong).
Destroy All Monsters
Godzilla vs Biollante -
I think this movie has some of the best tension, special effects and storyline of the Godzilla series (not necessarily, the spiritual element, but definitely the bio-espionage, hostage situation and psychic stuff). I think this is too low.
Godzilla vs King Ghidorah
Godzilla vs Mechagodzilla II
Godzilla vs Megaguirus
Invasion of the Astro-Monster -
Again, another Golden Age movie getting snubbed. Only really bad this time.
Godzilla Raids Again -
I'm not too passionate about this one, but I think it should be a lot lower than this.
Godzilla vs Mechagodzilla -
Mechagodzilla is ranked so low! This movie has spies, aliens, awesome fights, a great foe. Why is this movie ranked so low???
Terror of Mechagodzilla -
I think this was a great send off for the Showa series. Definitely an improvement on GvMG and that movie is already too low.
Godzilla 1985 -
Considering this is one of my favorite Godzilla movies, this is also too low. I can't help but think this has to do with the Americanization and not the Japanese film.
King Kong vs Godzilla
Godzilla vs Mothra: Battle for the Earth -
This film is already ranked low, but I watched this again on Sunday and absolutely hated almost everything about it. This film deserves to be lower, specially with what it's surpassing.
Godzilla 2000 -
This is a really fun, almost underrated Godzilla film. The special effects aren't the greatest, but now that it's older I have an appreciation for them. Too low.
Godzilla vs the Smog Monster -
This is the most unique Godzilla film. It's in my top 15, and is too low.
Godzilla vs Gigan -
This might be slightly too low, but I definitely don't love this film by any means. I cannot get past the stock footage and Godzilla falling apart. I guess some of the characters are okay, but I still don't think it salvages the movie.
As for the remaining:
Godzilla vs Space Godzilla -
This is my least favorite Godzilla film. Anything above the very bottom is too high.
Godzilla (1998) -
Pleasantly surprised how low this came out in the end. I still think it's worse than everything below it except for Megalon.
Son of Godzilla
Ebirah, Horror of the Deep -
I think this is one of the better of these movies. Again, Godzilla's design, the lack of destruction, and the special effects can't be salvaged by the plot which I also only think is okay. I don't think it's in the bottom five, but I don't think it's that good either.
Godzilla's Revenge
Godzilla vs Megalon