My friend Google found this highly technical article, "Practical Game Performance Analysis Using Intel® Graphics Performance Analyzers", which goes pretty much straight over my head, but when I see things like: "Objects rendered using a pixel shader may experience a processing bottleneck for the last batch of pixels from the pixel shader, since earlier fragments are rendered as the geometry is output from the rasterizer. Finally, use of Microsoft DirectX* (DX) locks and graphics processor unit (GPU) queries may transfer bottlenecks from one stage of the rendering pipeline to another", I get the impression that using pixel shaders can potentially slow things down, especially if the software you are running is not optimized for the pixel shader on your hardware.
Maybe someone who knows more, way more, than I do (which, let's face it, isn't asking all that much

), can make more sense of this.
In the meantime, I'll try playing with them off, and report back if I notice anything.
http://software.intel.com/en-us/articles/practical-game-performance-analysis-using-intel-graphics-performance-analyzers/