Doxygen is a bit slow - it takes about a couple of minutes to process my whole project, so for small incremental changes this is longer than actually building the rest of my
There is a DOT_NUM_THREADS options which may increase the performance on multicore machines. Unfortunately doxygen itself is just single threaded.
Another approach would be to organize your code into modules run for each module a separate doxygen instance and link the resulting tags together: http://www.doxygen.nl/manual/external.html