start /low /affinity 0x0e minerd.exe --threads 3 ...
I have a four-core machine, so I create three threads, and affinity is set to cores 2, 3, 4 (i.e. 0x02 | 0x04 | 0x08 = 0x0e). You might also want to set the affinity of the GPU miner to the first core in a similar fashion.
By restricting GPU mining to core 1, and CPU mining to cores 2 and 3, I can get both 250 MH/s for BTC and 8.5 kH/s for LTC...