Mark Jacobson, Stanford University professor of civil and environmental engineering, lists the top energy sources, from best to worst:

The top electrical generating energy sources are:

1. Wind
2. Concentrated Solar Power (CSP)
3. Geothermal power
4. Tidal power
5. Solar photovoltaics (PV)
6. Wave power
7. Hydroelectric power
8. Nuclear power
9. Coal (even with Carbon Capture and Sequestration, CCS)

Nuclear and coal actually tied for last place.

Read more from the Energy and Environmental Science Journal. For the non-academic, less-geeky version, Grist.org has a good summary.

Here's Jacobson discussing carbon dioxide: