We report the detection of [Ne II] emission at 12.81 micron in four out of the six optically thick dust disks observed as part of the FEPS Spitzer Legacy program. In addition, we detect a H I(7-6) emission line at 12.37 micron from the source RXJ1852.3-3700. Detections of [Ne II] lines are favored by low mid-infrared excess emission. Both stellar X-rays and extreme UV (EUV) photons can sufficiently ionize the disk surface to reproduce the observed line fluxes, suggesting that emission from Ne+ originates in the hot disk atmosphere. On the other hand, the H I(7-6) line is not associated with the gas in the disk surface and magnetospheric accretion flows can account only for at most ~30% of the observed flux. We conclude that accretion shock regions and/or the stellar corona could contribute to most of the H I(7-6)emission. Finally, we discuss the observations necessary to identify whether stellar X-rays or EUV photons are the dominant ionization mechanism for Ne atoms. Because the observed [Ne II] emission probes very small amounts of gas in the disk surface (~10^{-6} Jupiter masses) we suggest using this gas line to determine the presence or absence of gas in more evolved circumstellar disks.