In the first part of this thesis, we use a multi-model framework to examine a set of possible future energy scenarios resulting from R&D portfolios of Solar, Nuclear, Carbon Capture and Storage (CCS), Bio-Fuels, Bio-Electricity and Batteries for electric transportation. We show that CCS significantly complements Bio-Electricity, while most of the other energy technology pairs are substitutes. From the probabilistic analysis of future energy scenarios we observe that portfolios with CCS tend to stochastically dominate those without CCS; portfolios with only renewables tend to be stochastically dominated by others; and that there are clear decreasing marginal returns to scale. We also find that, with higher damage risk, there is more incentive for technical advancement in CCS and less incentive for development of Solar energy technology. In the second part of this thesis, we examine the optimal R&D portfolio changes at the different R&D budget levels and how risk in climate damages affects the optimal R&D portfolio. We find that the optimal portfolio is generally not robust to risk, and the optimal investments in the energy technologies vary with risk in climate damages; however R&D investments in certain energy technologies, such as Nuclear, are robust under the different risk cases. We note that while CCS plays a significant role in the optimal portfolio when there is no risk in climate damages, it plays an even more significant role in the higher climate damage risk cases. We also find that R&D investment in the Biofuels energy technology increases significantly with increase in climate damage risk, while Solar, Batteries for Electric Transportation and Bio-Electricity technologies go out of favor with increases in climate damage risk. We also propose a methodology for obtaining solutions to subset portfolio problems, based on the characteristics of the individual technologies. We prove that the subset portfolio problem is optimal if the individual technology does not interact with any of the other technologies, we confirm this in our empirical portfolio problem. In the third part of this thesis, we conduct an illustrative global sensitivity analysis on a large scale integrated assessment model with a view to determining the primary drivers of uncertainty in the model and examining the effect of structural uncertainty on the model. We compare our results to a previous paper which conducted a one factor at a time sensitivity analysis and find that both sensitivity methods provide the same result which is different from findings from the previous paper. We find that model interactions are present even in our very limited illustrative analysis. We also conduct most of the steps needed for a full global sensitivity analysis of the model and highlight the challenges in conducting this analysis on the GCAM model. We show that there exist a need for global sensitivity analysis for accurate determination of the principal drivers of uncertainty in integrated models.