GPGPU stands for General Purpose Graphics Processing Unit.
In recent years, the potential of powerful graphics processing units to carry out more resource demanding tasks has been highlighted. In some cases, GPUs prove to carry out operations much much faster than their CPU equivalents.
One such example is Folding@Home, where modified clients will exploit both ATI and NVIDIA graphics chips for their calculating potential. In doing so, the GPU can do the work much faster and this shows in the stats available on the Folding@Home website.