Abstract Using 16,421 spectra from a sample of 340 quasars (1.62 < z < 3.30) from the Sloan Digital Sky Survey (SDSS) Reverberation Mapping Project, we present an analysis of quasar spectral variability. We confirm the intrinsic Baldwin effect (BE) and brighter-means-bluer trends in which emission line strength and color are associated with changes in luminosity. We then create a composite differential spectrum that captures the wavelength dependence of quasar variability as a function of change in luminosity. When using a bandpass around 1740 Å to describe the luminosity, the differential spectrum follows a power law at longer wavelengths that breaks blueward of 1700 Å. However, the shape of the differential spectrum, the location of the power-law break, and the slope of the intrinsic BE all vary with the choice of bandpass used to define the change in quasar luminosity. We propose that the observed behavior can be explained by inhomogeneous accretion or slim accretion disk models where delays in the reprocessing of incident light on the accretion disk cause local deviations in temperature from the thin-disk model. Finally, we quantify the effects on cosmology studies that are due to the variations in the quasar spectrum in the Lyα forest wavelength range. Using the observed spectroscopic signatures to predict the quasar continuum over the interval 1040 < λ < 1200 Å, we find that the derived spectral templates can reduce the uncertainty of the Lyα forest continuum level in individual epochs from 17.2% to 7.7%, near the level where systematic errors in SDSS flux calibration are expected to dominate.