It depends upon what you mean by discrete. When you're talking about particles, in Fourier space, one waveform is a specific momentum. So, if you're describing particles with definite momentum, the Fourier representation is exact.
And for another example where Fourier transforms are excellent, take the early universe. The early universe can be well-described by linear theory, which makes it amenable to Fourier analysis. When one does the analysis based upon some particular theory, one obtains a specific statistical distribution of overdensities and underdensities in the universe, which can be best-measured by observing the hot/cold spots on the cosmic microwave background.
Another, more down to Earth, example comes about from looking at AC circuits: when you're dealing with alternating current driven by a sinusoidal waveform, it becomes extremely convenient to use Fourier analysis.