They are programmed the way shared memory parallel machines have been used since time immemorial in the HPC world. Hundreds of cores is normal there. The same Intel software stack (OpenMP, Threaded Building Blocks, parallel Fortran etc) is used, same one that Intel markets for regular HPC.
Yeah, you have slower cores and the SIMD is twice as wide, but its main selling point is that you get to keep the regular programming model - unlike with NVidia or AMD. Along with benefits that come with it (mature software, openness, etc).
See eg. Intel's Xeon Phi Programmin Guide for an intro: http://software.intel.com/sites/default/files/article/330164...