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This depends on which story you're watching/reading etc.

Before "The Three Doctors", the Doctor thought that Omega was a myth. In "The Three Doctors", the Doctor considers Omega to be a danger to the universe.

In some later stories, the Doctor feels some sympathy for Omega, but recognises that he still poses a danger to the universe.

In the Virgin novels, and only the Virgin novels, the Doctor and Omega knew each other thousands of years ago, and worked together(along with Rassilon) to create Time Lord society.