Orga (incase you didn't know ;) ).
He's just so vastly different compared to the usual Godzilla foe. I mean, he EATS monsters! Also, watching the film more than 100 times, I noticed he does not immediately attack Godzilla. He seems to analyze his attcker's moves and situation. I also have a thing for knuckle-walkers. ;)
There's a personal reason why I love Orga too. He was the first Godzilla villain I have ever seen. And I actually liked him better than Godzilla. I wanted Orga to win! I got the roaring Orga figure immediately after I saw Godzilla 2000, and carried him around with me for years on end! I know it sounds cheesy and frankly creepy, but Orga was my friend when I had none (I have serious social anxiety...).
I now know that Godzilla is the ultimate monster in history, but right behind him is my man Orga! :)