The right answer is probably "it depends".
For pure comparative performance between code run on different platforms, I usually count transcendentals, sqrt, mads, as one operation. In that sort of situation, the key performance metric is how long the code takes to run. It is almost impossible to do the comparison any other way - how would you go about comparing the "FLOP" count of a hardware instruction for a transcendental which takes 25 cycles to retire, versus a math library generated stanza of fmad instructions which also takes 25 cycles to complete? Counting instructions or FLOPs becomes meaningless in such a case, both performed the desired operation in the same amount of clock cycles, despite a different apparent FLOP count.
On the other hand, for profiling and performance tuning of a piece of code on given hardware, the FLOP count might be a useful metric to have. In GPUs, it is normal to look at FLOP or IOP count and memory bandwidth utilization to determine where the performance bottleneck of a given code lies. Having those numbers might point you in the direction of useful optimizations.
