in the gear that is closest to the 1:1 gear ratio
the reason for the dyno in the 1:1 gear ratio is due to the Dynojet. Dynojet mathematically creates a horsepower number based on mass (which is the known weight of the rollers) and accleration (how fast the car is accelerating the known weight).
From force (F), we can calculate horsepower.
Dyno the car in 2nd gear, and acceleration (a) goes way up, causing force (F) to go way up.
So by dynoing the car in the gear closest to the 1:1 gear ratio, we eliminate any acceleration advantage or disadvantage caused by the transmission, which gives us unskewed whp numbers (even though Dynojet has a fudge factor in there which makes them skewed anyways and read high).
As for other dynos out there (i.e. Mustang and Dyno Dynamics) - they use a load cell to measure roll force (the amount of force the tire is placing on the roller). Based on roll force and the radius arm going to the load cell, we get roll torque. Based on roll torque and roll speed, we can get vehicle horsepower. Vehicle horsepower and vehicle RPM gives vehicle torque. It doesn't matter what gear you run in on load cell style dynos as they are measuring force, not acceleration. Force does not change from gear to gear.