It doesn't really matter what program you use to measure as long as you're using a calibrated mic. Like warnerwh noted, the Behringer units work well (I also use a DEQ2496 with an ECM8000 mic). The ECM8000 mic is calibrated but requires phantom (12V) powering, which the DEQ2496 can provide.
Also note that a unidirectional mic should be used if possible to avoid heavily altered frequency response of omnidirectional mics have (no good if you're measuring responses at your listening position, which comes from all around you, not just in front).
Hope that helps.