Manhattan wins. He could BFR Doomsday without issues. Also, DD was good at absorbing energy directed at him, but not sure he would hold up so well if Manhattan just exploded/disintegrated/tore him apart mentally. We know that he can be hurt, as seen when WW removed one of his limbs. In contrast, even if Doomsday damages/destroys Manhattan's form, he can just make a new one.
Originally posted by CPT Space BombAgain, Manhattan wins without BFR. Anyone with matter transmutation/manipulation on a molecular level wins. There are just too many ways he can kill Doomsday without needing to bfr.
Dr Manhattan in an absolute stomping. Manhattan doesn't even need Kryptonite. He could just turn DD's molecules into my little ponies and then send them to New Jersey.