The following code sample comes from "Juice Up Your App with the Power of Hyper-Threading", an MSDN article:

public void SetProcessAffinityToPhysicalCPUForHyperthreadOnly(int processid)
{
    int res;
    int hProcess;
    int ProcAffinityMask = 0, SysAffinityMask = 0;
    hProcess  = OpenProcess(PROCESS_ALL_ACCESS, 0, processid);
    res = GetProcessAffinityMask(
        hProcess, ref ProcAffinityMask, ref SysAffinityMask);
    if (SysAffinityMask == 3) // 1 proc, 2 logical CPUs
        res = SetProcessAffinityMask(hProcess, 1);
    else if (SysAffinityMask == 15)  //dual proc, 4 virtual CPUs
        res = SetProcessAffinityMask(hProcess, 3);
    res = CloseHandle(hProcess);
}

From the sample above, we see that the affinity mask is such that all physical processors come first in the mask, then the logical (Hyper-threaded) processors.

If your process is a heavy user of floating point instructions, setting the affinity mask to (number of processors/2) - 1 will make sure your threads will give preference for the physical processors which have FPU.

For a sample on how to detect if Hyper-Thread is on in C/C++, you could use this:

__inline BOOL hyperThreadingOn()
{
    DWORD       rEbx, rEdx;
    __asm {
         push   eax         // save registers used
         push   ebx
         push   ecx
         push   edx
         xor    eax,eax     // cpuid(1)
         add    al, 0x01
        _emit   0x0F
        _emit   0xA2
         mov    rEdx, edx   // Features Flags, bit 28 indicates if HTT (Hyper-Thread Technology) is
                            //  available, but not if it is on; if on, Count of logical processors > 1.
         mov    rEbx, ebx   // Bits 23-16: Count of logical processors.
                            //             Valid only if Hyper-Threading Technology flag is set.
         pop    edx         // restore registers used
         pop    ecx
         pop    ebx
         pop    eax
    }
    return (rEdx & (1<<28)) && (((rEbx & 0x00FF0000) >> 16) > 1);
}