I'm working on a Ph.D. working in GPU architecture, and this course is the real deal. It goes beyond how to run things on a GPU to analyzing the runtime and work efficiency of algorithms suited to the GPU.
Wen-mei Hwu's lectures on "Advanced Algorithmic Techiques for GPUs" (first lecture slides: http://iccs.lbl.gov/assets/docs/2011-01-24/lecture1_computat...) are a gold mine of GPU programming techniques. I believe he has published several books on the topic too, and released a benchmark suite (Parboil http://impact.crhc.illinois.edu/parboil/parboil.aspx) optimized with these techinques.