IAT makes a decent difference if you monitor your AFR's. I had my IAT sensor go bad on me and not only did it end up drawing more power (meaured via voltmeter) but it also threw a CEL. Although it is not vital to your car operating, it is meant to be part of the closed loop control system so it's best to leave it in a location like stock. I had the MAF relocated on my old P5 with the IAT in a like-stock location and I always wondered if some of the relocated-related issues could be solved if the IAT could somehow be moved to the pressure sure near the MAF like stock. Also, if IAT's start to read too high it can cause your engine to start dumping fuel (measured via wideband during long trips through mountains) in attemps to cool engine temperatures.
Short answer, leave it in the intake pipe. You may not notice a difference, but it's how the system is supposed to work.