If you want to be really efficient and you have enough time to spent, use SIMD instruction.
You can compare several pairs in one instruction:
r0 := min(a0, b0)
r1 := min(a1, b1)
r2 := min(a2, b2)
r3 := min(a3, b3)
__m64 _mm_min_pu8(__m64 a , __m64 b );
Today every computer supports it. Other already have written min function for you:
http://smartdata.usbid.com/datasheets/usbid/2001/2001-q1/i_minmax.pdf
or use already ready library.