I have to go with Thanos and Darkseid on this one. If we are talking Old Thanos and not DC52 Darkseid.
Old Darkseid had the Anti-Life Equation as well as his whole planet for prep. Thanos scientific genius and rescources should be able to trump Doom's prep as much as I like him. Ultron is a thread but there is no reason why Darkseid couldn't be able to shut him down.
Thanos and Darkseid so easily, not sure about Thanos but Darkseid is fantastic with prep. His prep was essential in beating 2 of the biggest threats to the DC universe and then there was what he was able to accomplish while dying in final crisis.
Thanos and Darkseid win. Ultron at his best was an interplanetary threat during Phalanx. Doom can do a lot within 3 months, but he is not taking out both Thanos and Darkseid even with Ultron's tech. Especially since Thanos Doom under constant surveillance and he will know everything that Doom is planning
Thanos and Darkseid are probably the most powerful villains in their respective universes, Doom is great with prep and Ultron is pretty remarkalble but cmon him and ultron vs Thanos AND darksied? there is just too much power there