Yeah, the ending to Son of Godzilla had me going. I seriously think that SoG was the only Godzilla film that I actually cried to.
I don't remember if I cried at the ends of The Return of Godzilla nor Godzilla vs. Destoroyah - I still bash on Kawakita for the whole meltdown death idea. I personally think that Godzilla's death in Godzilla vs. Destoroyah could have been handled a lot better than it did. I found myself feeling more sympathetic towards Junior's death rather than Godzilla's... but it still did not have me tear up.