Let me be clear: Conjectures are untested ideas. Prejudices, in the sense of this blog, are wrong ideas that people continue to hold.
The list of prejudices on the right gives wrong ideas. The are known to be wrong.
Take the idea that space is made of points. If we combine general relativity and quantum gravity, we know that at small distances, space is decribed by quantum foam. We do not know how to describe quantum foam (do you have any conjecture?); but one thing is sure: space is not made of points, and nicely arranged in three dimensions.
Take the idea of supersymmetry. Every single prediction it made (sparticles, light Higgs, high electric dipole moments, new decays, new reactions) contradicts experiment. Supersymmetry is wrong.
Take the idea of GUTs. Every single prediction they made contradicts experiment. GUTs are wrong.
Bill K writes that theoreticians should word on conjectures. I agree. But they should not work on wrong ideas. Bill K's comment could be read to suggest (though he is not so clear on this point) that it is ok to work on wrong ideas if one has no correct ones. Well, the point of this blog is that a way to find the correct ideas is to get rid of the wrong ones. Riding dead horses does not help.
I take the approach of Peter Woit to its logical completion. Let's get rid of all wrong ideas. Not only string theory, but also the other ones. Woit did not present an alternative to string theory, but we cannot blame him for that. His aim is to point out what is wrong.
My hope goes further. If we point out all wrong ideas, there is so little left that we will get into a crisis. And then only will we find the right idea. I like crises. They are chances for progress. Of course, people have all the right not to like crises, and have all the right to cling to false ideas. Mike Duff is a good example. So is Lubos Motl. But that is not where progress will come from. (And anyway, I think they will change their mind as soon as they see that their ideas do not work.)
If you like solving problems, you will remember that before finding a solution, you are in a sense of confusion. During the confusion state you are tense. After the solution appeared, you are relaxed. The tense confusion state is the crisis situation. If we want to find the solution, we need a crisis first. If we keep on saying that we have the solution while we have not, we are taking the wrong path.