Not available

Showa:

3. Terror Of Mechagodzilla

2. Godzilla VS Mechagodzilla

1. Godzilla 1954

Heisei (The best era):

3. Godzilla VS Mothra: Battle for Earth

2. Godzilla VS Space Godzilla

1. Godzilla VS King Ghidorah

Millennium:

3. Godzilla 2000

2. Godzilla: Final Wars

1. GMK  

It's hard for me to break down my favorites by era if I'm considering Godzilla and non-Godzilla kaiju films. So I guess I'd have to make two separate lists: one for Godzilla films, and one for non-Godzilla films.

Godzilla Series

Showa:

3. Godzilla vs. Mechagodzilla

2. Invasion of Astro-Monster

1. Mothra vs. Godzilla

Heisei:

3. Godzilla vs. King Ghidorah

2. Godzilla vs. Biollante

1. Godzilla vs. Mechagodzilla II

Millennium:

3. Godzilla 2000: Millennium

2. Godzilla Against Mechagodzilla

1. GMK

Other

Showa:

3. Latitude Zero

2. War of the Gargantuas

1. Mothra

Heisei:

3. Gamera the Brave

2. Gamera 2: Attack of Legion

1. Gamera 3: Revenge of Iris

Even with two lists, it was hard to narrow my favorite films by era to just three. There are so many great non-Godzilla kaiju films in Toho's Showa library, and every single Heisei Gamera film ranks up with my all-time favorites. I suppose I should at least give an honorable mention to Rebirth of Mothra, which would be my favorite Heisei kaiju film outside of the Gamera or Godzilla series.

Sort of racking my brain on this one. Whatever it is, it won't be in order. That said I highly, highly agree with some of Godzilla: King of the Monsters' choices since he propped up my top 3 favorites in the entire series.

I do find this format of listing the movies much easier though. When people ask me to list the entire series I typically scoff. 30+ movies from different eras, by different filmmakers with different themes and styles? It gets hard to compare and in some ways the exercise devalues the merit of each individual movie.

I like this chopped up format better. It gives us more to consider about each film.

My reply to the original post's question still pending...

In no order just top 3s, and only Godzilla ones since I haven't watched any of the others in over a year.

Showa

1. Monster Zero

2. Godzilla vs MechaGodzilla

3. Terror of MechaGodzilla

Heisei

1. Godzilla vs Destoroyah

2. Godzilla vs Biollante

3. Godzilla vs King Ghidorah

Millennium

1. Godzilla 2000

2. Tokyo SOS

3. Godzilla against MechaGodzilla