I think I am leaning towards blue and gold as the two front runners for Jedi!Dooku's lightsaber. I nixed purple from my shortlist because that's Mace's signature saber color, and I don't think I'd use green because that would make Dooku's duel with Yoda less visually dynamic.

If he has a blue saber, then in Revenge of the Sith when he duels Anakin, the two blue lightsabers could be a bit of a foreshadowing to when Anakin duels Obi-Wan. However, gold would save the visual of two like-colored sabers clashing for the climax of ROTS, and in addition to making the duels more visually dynamic it would also give Dooku a unique signature. However, as has been said, giving him a unique lightsaber would potentially make the ambiguous nature of his character a little too obvious, but that's debatable.

Anyway, here are two manips I did in Photoshop.

So, blue is probably the way to go, but gold still has potential IMO.