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1. Godzilla Rulers of Earth (without a doubt)

2. Godzilla Rage Across Time

3. Godzilla Ongoing/History's Greatest Monster

4. Godzilla Kingdom of Monsters

5. Godzilla in Hell

6. Godzilla Cataclysm 

7. Godzilla Half-Century War

8. Godzilla Legends

9. Godzilla Oblivion

10. Godzilla Gangsters & Goliaths

Honestly, I think these are all of IDW's Godzilla Graphic Novels. I hope they make more soon. All of theirs are very good.

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I have yet to read "Rage Across Time" yet, but I really want to.

My top three are Rulers of Earth, Half-Century War and Legends. I wasn't a fan of either Kingdom of Monsters and the ongoing sequel.

Also, as I understand it, IDW hasn't exactly lost the rights, but due to some disputes have decided to put their Godzilla line on hiatus indefinitely. They'll probably just end letting their rights lapse as a result.