I created a new page on the wiki to collect links like the Big Scary Idea one: Criticism of the sequences. If anyone knows of more links to intelligent disagreement with ideas prevailing on Less Wrong, please add them!
Wasn't there a professional physicist who criticizes something specific in Eliezer's QM sequence? Can't remember where...
Also, not sure if these count, but:
Many people complain that the Singularity Institute's "Big Scary Idea" (AGI leads to catastrophe by default) has not been argued for with the clarity of, say, Chalmers' argument for the singularity. The idea would be to make explicit what the premise-and-inference structure of the argument is, and then argue about the strength of those premises and inferences.
Here is one way you could construe one version of the argument for the Singularity Institute's "Big Scary Idea":
My questions are: