The top two current supercomputers do, in fact, use APU accelerators: http://www.top500.org/blog/lists/2013/06/press-release/

The Tianhe-2 (~34 PetaFlops) uses 48,000 Intel Xeon Phi co-processors, with 63 cores each.  The Phi is designed similar to a graphics card, but instead of the cores being optimized for graphics pipeline, they are optimized for general purpose math.  Titan (~17.5 Petaflops) uses 256K x Nvidia K20x cards, which uses the same GK-110 graphics chip as their top end consumer card.  The only real difference is the scientific card uses error correcting memory, and the consumer card doesn't, because dropping a few bits here and there in rendering a video game doesn't matter, but in doing scientific problems it does.