The Hilbert-Huang transform (HHT) is a new method for the analysis of nonstationary signals that allows a signal's frequency and amplitude to be evaluated with excellent time resolution. In this paper, the HHT method is described, and its performance is compared with the Fourier methods of spectral analysis. The HHT is then applied to the analysis of molecular dynamics simulation trajectories, including enhanced sampling trajectories produced by reversible digitally filtered molecular dynamics. Amplitude-time, amplitude-frequency, and amplitude-frequency-time spectra are all produced with the method and compared to equivalent results obtained using wavelet analysis. The wavelet and HHT analysis yield qualitatively similar results, but the HHT provides a better match to physical intuition than the wavelet transform. Moreover the HHT method is able to show the flow of energy into low-frequency vibrations during conformational change events and is able to identify frequencies appropriate for amplification by digital filters including the observation of a 10 cm(-1) shift in target frequency.