RPM is always noisy. It seems to be true for more than just our stock ECUs as well. I've seen it on a few other engine management systems, even on other cars. I suspect it is just because RPM is logged as an instantaneous measure, and the ECU is calculating RPM as an incredibly high speed (possibly several times per crank rotation even at high RPM). The crank is not rotating at a uniform speed. It could also be due to inaccuracy in how RPM is calculated, but I tend to lean towards the extreme speed hypothesis. Flywheel inertia could play a part.
So, basically you have to smooth the data.
Here's some playing I did with different window functions to create a road dyno, though I never bothered to finish it. It needs all the factor labels and units of measure worked out, maybe some sort of wind resistance and friction compensation, and a lot of polish. You can at least get the idea on the window functions.
http://freon.shackspace.com/car/ecu%20a ... adDyno.xls