Recent work with the Spitzer Space Telescope shows that emission from water and organic molecules is commonly found in the mid-infrared spectra of disks surrounding young stars. As these diagnostics probe the inner planet formation region of the disk (within a few AU), they offer the opportunity for new insights into planet formation processes and disk chemical evolution. I will describe how such spectra can be used to study whether disks synthesize and preserve molecules and how they might be used to obtain evidence of the planet formation process in action.