tldr
pre-crisis superman would of rofl stomped goku with vegeta fusion ssj4..sorry but its true..i dont even like superman but before crisis he was like 1000 gogetas ssj4..srsly..he dragged solar systems around, blew up galaxies with a sneeze..it was dumb..they had to NERF him drastically to have any villains..
after crisis goku wins, however i think doomsday vs goku, doomsday wins, goku can kill him 1000 times it won't matter hes immortal and adapts to whatever killed him, doomsday died "a billion deaths" to get on supermans level, then died to superman then rofl stomps superman, then they made it where doomsday was weakened by kryptonite, but unlike superman it only caused him pain, where as superman can die from it
goku might kill doomsday but after that doomsday becomes immune to w/e form goku used
you know how they got rid of doomsday? they teleported him into the future right before time ended..TIME HAD TO END to kill doomsday, and he still came back after that (lex cloned)