When attempting to determine what frequencies contribute the most to the variance of a process my research group relies heavily on multitaper spectral estimation techniques. This involves estimating multiple spectra with different tapers / windows and using the weighted average as the overall estimate.
Specifically, we use Discrete Prolate Spheriodal Sequences (DPSS's or Slepian sequences (named after their "discoverer")) as our windows because they are doubly orthogonal and provide an optimal trade off between bias and variance (Spectrum Estimation and Harmonic Analysis - DJ Thomson - 1982).
One method to determine which frequencies are important is the harmonic F-test which determines "how sinusoidal" a particular frequency is in the data. There are other methods that can be used, the harmonic F-test is one of the more simple.
R has a software package "multitaper" and Matlab has the function "pmtm()". This method of estimation is parametric in the sense that in order to compute the windows, one parameters must be assigned: NW (the time bandwidth parameter) which is normally 3 < NW < 20 (for most purposes I have seen it is defaulted to 4). This parameter sets the width of the window (W) based on the amount of data that is available (N). Lastly, you must decide how many windows you would like to use (K) where K <= floor(2*NW-1). The tapers after 2*NW actually concentrate power outside of -W to W.
If you use the multitaper package in R, the defaults are all set and you can get a general idea of the spectrum with very little tinkering.