Question

Im starting with an array of 100,000 bytes where only the lower 6 bits in each byte have useful data. I need to pack that data into an array of 75,000 bytes as fast as possible, preserving the order of the data.

unsigned int Joinbits(unsigned int in) {}

Answer 1

// 00111111 00111111 00111111 00111111
//   000000   001111   111122   222222
void pack6(
  register unsigned char o, 
  register unsigned char const *i, 
  unsigned char const *end
) 
{
  while(i!=end)
  {
    *o++ =  *i          << 2u | *(i+1) >> 4u; ++i;
    *o++ = (*i & 0xfu)  << 4u | *(i+1) >> 2u; ++i;
    *o++ = (*i & 0xfcu) << 6u | *(i+1)      ; i+=2;
  }
}

Will fail if input length is not divisible by 4. Assumes high 2 bits of input are zero.
Completely portable. Reads 4 input bytes 6 times, so 50% inefficiency on reads, however the processor cache and compiler optimiser may help. Attempting to use a variable to save the read may be counter-productive, only an actual measurement can tell.