This paper investigates long-term transitions of the global energy system compatible with realizing low stabilization climate targets, using an enhanced MERGE model. The results indicate that stringent mitigation targets can be met under many technology scenarios, but major technological change is needed, highlighting important roles for R&D and learning-by-doing. The analysis explores the impact of limiting the set of available technology options (to account for technical uncertainties and issues of public acceptance) and identifies important influences on energy system development and economic costs under low stabilization. Biomass availability is seen to have a major influence on the characteristics of the energy system. Carbon capture and storage technologies also prove to be potentially critical for both electricity and fuel synthesis, particularly when combined with biomass to produce net negative emissions. Additionally, the availability of fast breeders provides a competitive zero-emissions option. Energy efficiency and large-scale application of renewables are also critical to realising low stabilization scenarios.