The rev limit changes as does the base idle speed. I overclocked my own ECU in an effort to get a better/smoother idle with aftermarket cams. As Pat said, it's not widely known what else changes.
I have a pretty good feeling that things like knock/misfire detection are "altered" a little bit... Based on the ECU seeing X number of 'noise' incidents in Y number of clock cycles.
If the clock cycle is faster but the engine isn't running faster, then this will basically make the ECU slightly less sensitive to misfire incidents, or in my case, false misfire detections due to lw flywheel and cams combination.
I also believe that the IAM (ignition advance multiplier) will lean towards the advance side and will also get there more quickly from an ECU reset.
However, I've got no way to prove my theories, so don't take them as gospel =]