The new GISS composition and climate modeling system has been used for a wide variety of studies during the past two years, including simulations for the forthcoming IPCC 2007 Assessment. I will discuss the response of tropospheric ozone and hydroxyl to changing emissions and climate both in our model and over the range of the 25 IPCC models. The IPCC models included tropospheric composition only, however. I will present results from our 'full atmosphere' (surface to mesosphere) composition model showing the sensitivity of stratospheric composition and stratosphere-troposphere exchange to climate, and how this affect projections in the troposphere. I will also report on simulations of carbon monoxide in the troposphere, and comparisons with MOPITT and other satellite observations. Those results provide substantial evidence for long-range transport of pollution lasting for multiple years. Finally, I will present results of simulations of methane levels during various Holocene and glacial periods and discuss how these results can be used in combination with ice core methane records to constrain paleo sources and sinks