Gas-giant planets emit a large fraction of their light in the mid-infrared ($gtrsim$3$mu$m), where photometry and spectroscopy are critical to our understanding of the bulk properties of extrasolar planets. Of particular importance are the L and M-band atmospheric windows (3-5$mu$m), which are the longest wavelengths currently accessible to ground-based, high-contrast imagers. We present binocular LBT AO images of the HR 8799 planetary system in six narrow-band filters from 3-4$mu$m, and a Magellan AO image of the 2M1207 planetary system in a broader 3.3$mu$m band. These systems encompass the five known exoplanets with luminosities consistent with L$rightarrow$T transition brown dwarfs. Our results show that the exoplanets are brighter and have shallower spectral slopes than equivalent temperature brown dwarfs in a wavelength range that contains the methane fundamental absorption feature (spanned by the narrowband filters and encompassed by the broader 3.3$mu$m filter). For 2M1207 b, we find that thick clouds and non-equilibrium chemistry caused by vertical mixing can explain the objects appearance. For the HR 8799 planets, we present new models that suggest the atmospheres must have patchy clouds, along with non-equilibrium chemistry. Together, the presence of a heterogeneous surface and vertical mixing presents a picture of dynamic planetary atmospheres in which both horizontal and vertical motions influence the chemical and condensate profiles.