I don't mind 3D if I feel it adds something to the experience. Up to this point I think Avatar has been the best 3D movie I have seen, it worked brilliantly with the visuals and provided an extremely immersive experience.
In my opinion 3D is best used in movies that present a new world to the audience such as Tron Legacy, Avatar or even Alice in Wonderand even though it wasn't good. I don't mind seeing a movie in 3D if it is filmed using the 3D cameras or if the conversion is top notch. But if it is a film like the Avengers or Pirates of the Caribbean it is not really necessary, and I only watch it in 3D to get the IMAX screen.
However I feel that Prometheus falls into the category of movie that would be good in 3D. Not only has it got gorgeous visuals based off the trailers, but it is also shot in 3D (I think). It is also the first horror film I will see in 3D so I think the added layer of immersion will make it seem scarier.
By the way, I am seeing the midnight screening on release which is less than a day after the premier so I will be watching it without knowing what the critics think of it, so I will come online and give mine and my friends impressions (without spoilers) on the first of June, for those abroad.