  The atmospheric pressure-temperature profiles for transiting giant planets
cross a range of chemical transitions. Here we show that the particular shape
of these irradiated profiles for warm giant planets below 1300 K lead to
striking differences in the behavior of non-equilibrium chemistry compared to
brown dwarfs of similar temperatures. Our particular focus is H$_2$O, CO,
CH$_4$, CO$_2$, and NH$_3$ in Jupiter- and Neptune-class planets. We show the
cooling history of a planet, which depends most significantly on planetary mass
and age, can have a dominant effect on abundances in the visible atmosphere,
often swamping trends one might expect based on Teq alone. The onset of
detectable CH$_4$ in spectra can be delayed to lower Teq for some planets
compared to equilibrium, or pushed to higher Teq. The detectability of NH$_3$
is typically enhanced compared to equilibrium expectations, which is opposite
to the brown dwarf case. We find that both CH$_4$ and NH$_3$ can become
detectable at around the same Teq (at Teq values that vary with mass and
metallicity) whereas these "onset" temperatures are widely spaced for brown
dwarfs. We suggest observational strategies to search for atmospheric trends
and stress that non-equilibrium chemistry and clouds can serve as probes of
atmospheric physics. As examples of atmospheric complexity, we assess three
Neptune-class planets GJ 436b, GJ 3470b, and WASP-107, all around Teq=700 K.
Tidal heating due to eccentricity damping in all three planets heats the deep
atmosphere by thousands of degrees, and may explain the absence of CH$_4$ in
these cool atmospheres. Atmospheric abundances must be interpreted in the
context of physical characteristics of the planet.
