Who was Godzillas most Powerful Enimes

Humans.

If we're just looking at kaiju, it would depend on era. King Ghidorah is a civilization destroyer, Biollante is immortal, and Keizer Ghidorah is the ultimate weapon of Planet X so take your pick really.

I all depends of which era and which incarnation. But if we are saying in general, I'd say Mothra, King Ghidorah, Monster X/Keizer Ghidorah, Destoroyah, and MechaGodzilla.

What about Hedorah?? I know it sounds weird but in the movie Godzilla struggled so much trying to get rid of him repetitively attacking him with Atomic breath in attempts to rid him from this plane of existence. 

Biollante would most definitely be included as she is immortal and pretty much was the reason that Space Godzilla was created. 

King Ghidorah cause I mean come on he has only been a main bad guy for ever. He has been on Earth, Planet X, and he has even been turned into Mecha King Ghidorah. 

Also I would love to think Gigan since he has always played a role in assisting other monsters with there destruction of earth and attempt to rid Godzilla. 

Destroyah, Ghidorah, Spacegodzilla, Orga.

Destoroyah and SpaceGodzilla

After seeing the final film in the anime trilogy, that film's version of Ghidorah, WITHOUT ANY DOUBT, is Godzilla's most powerful enemy.

He is literally nothing BUT absolute unfair hax that you can't do anything against unless you target what keeps him anchored to our universe.