Less Wrong has some material on this topic :)
Seriously though, I'd love to see some applied-rationality techniques put to use successfully doubting parts of the applied rationality worldview. I've seen some examples already, but more is good.
The biggest weakness, in my opinion, with purely (or almost purely) probabilistic reasoning is the fact that it cannot ultimately do away with us relying on a number of (ultimately faith/belief based) choices as to how we understand our reality.
The existence of the past and future (and within most people's reasoning systems, the understanding of these as linear) are both ultimately postulations that are generally accepted at face value, as well as the idea that consciousness/awareness arises from matter/quantum phenomena not vice versa.
If it's worth saying, but not worth its own post (even in Discussion), then it goes here.