It's been pointed out to me that hydroelectricity may be disputed as a "clean" energy source. In short: the flooding of reservoirs behind dams kills land plants, which decay and emit methane, which is a potent greenhouse gas. See:
http://en.wikipedia.org/wiki/Global_warming_potential
E.g., on the 20-year time scale, it's a 70 times more potent GHG than CO2. Very good at absorbing IR. This is why waste-to-energy (burning landfill gas) is actually climate-friendly - the waste methane emitted is much worse than CO2, so burning it, converting it to CO2, is actually a net improvement in the situation. But
other methane sources are too diffuse to capture, and may present dangerous positive feedbacks to runaway climate change.
Anyway, dam flooding and methane emissions - IPCC AR4 WG3 reviews the literature. From § 4.3.3.1, p. 273-4:
http://www.ipcc.ch/ipccreports/ar4-wg3.htm
High emissions of CH4 have been recorded at shallow, plateau-type tropical reservoirs where the natural carbon cycle is most productive (Delmas, 2005). Deep water reservoirs at similar low latitudes tend to exhibit lower emissions. Methane from natural floodplains and wetlands may be suppressed if they are inundated by a new reservoir since the methane is oxidized as it rises through the covering water column (Huttunen, 2005; dos Santos, 2005). Methane formation in freshwater produces by-product carbon compounds (phenolic and humic acids) that effectively sequester the carbon involved (Sikar, 2005). For shallow tropical reservoirs, further research is needed to establish the extent to which these may increase methane emissions.
Lots of variables. I would guess that the increased emissions in tropical forests are simply from the larger amounts of biomass decaying, but I don't know (the paper is closed-source). The effect of shallow water is probably just the the amount of power generated - deeper water = larger hydroelectric head = higher power density per area, which inversely means emissions/power are lower. A
Delmas paper abstract (2001, not his 2005 one referenced) also mentions N2O emissions as another GHG produced.
But quantities are what's important:
Several Brazilian hydro-reservoirs were compared using life-cycle analyses with combined-cycle natural gas turbine (CCGT) plants of 50% efficiency (dos Santos et al., 2004). Emissions from flooded reservoirs tended to be less per kWh generated than those produced from the CCGT power plants. Large hydropower complexes with greater power density had the best environmental performance, whereas those with lower power density produced similar GHG emissions to the CCGT plants. For most hydro projects, life-cycle assessments have shown low overall net GHG emissions (WEC, 2004a; UNESCO, 2006). Since measuring the incremental anthropogenic-related emissions from freshwater reservoirs remains uncertain, the Executive Board of the UN Framework Convention on Climate Change (UNFCCC) has excluded large hydro projects with significant water storage from the CDM. The IPCC Guidelines for National GHG Inventories (2006) recommended using estimates for induced changes in the carbon stocks.
So I tracked down "WEC 2004a"...
http://www.worldenergy.org/documents/lca2.pdf
This is its key figure, which compiles LCAs from other studies:

And there you have it: combined GHG emissions, normalized to equivalents of CO2 (basically, amounts multiplied by their global warming potential - see above). As the WG3 says, most of these hydro plants have
extremely low GHG emissions - about the same as the life-cycle emissions of wind turbines, and much lower than solar PV. The outlier, Petit Saut, is in the tropical rainforest of French Guiana (South America) - it's the subject of the Delmas 2001 paper I linked earlier. It's much higher, but still in the solar PV range (and *far* below natural gas - fossil fuels are off the chart). (N.B. nuclear has the lowest GHG emissions of all)
From page 35: Churchill is a series of dams with reservoirs, as is "Africa"; whereas La Grande and "Sweden" are run-of-the-river systems (no reservoir). The paper suggests run-of-the-river systems should have lower GHG emissions (no reservoir flooding --> no decay), which isn't visible in the data. Oh, and they also have Itaipu in there, and it's extremely clean, at 3.5-6.5 tCO2(eq)/GWh - this
despite having a large reservoir, in a tropical rainforest...?
Itaipu, of course - one of the world's largest dams, absolutely huge... powers 1/5th of Brazil
http://en.wikipedia.org/wiki/Itaipu