I think this has been said before:
Automatics: Dyno in OD from RPM where TCC stays locked and truck doesn't downshift
5-speeds: Dyno in 4th (1:1) under 400hp, 5th over 400hp.
6-speeds: Dyno in 5th (1:1) under 400hp, 6th over 400hp.
With the manuals, make the run as listed above, then, if under 400hp, make one last run in the higher gear. While the number will usually be lower, it will be your baseline for later testing, where the speeds will be the same.