Hyperthreading allows for the CPU to stay active and to never go idle during a load. Lifehacker made a nice post based off of from As fast As Possible's YouTube video explaining this technology by theory and metaphor. It is a nice read and Linus in the YouTube video does a great job explaining it.
If Hyperthreading is on, it keeps the processing more at a stable overall speed and makes workloads that don't require the processes to be consecutive (i.e. rendering in Blender, video editing, and heavy multitasking) a noticeable amount faster. While if your professes require them to be done in order (i.e. computation math equations) it my make no difference at all to a slight decrease in performance. I think that you would see at least a noticeable increase in performance in Folding@home, especially if you're running other tasks at the same time, but this would depend on the programming and optimization of the application. How ever much hyperthreading helps, it isn't the same as double the processing cores, but it is overall better to keep it on for much faster multitasking and risking the possible tiny decrease in productivity and performance once in a blue moon.
Hope it helps!