For all the talk of how plunging oil prices threaten the clean energy sector, it’s really the separate-but-related fall in natural gas prices that matters. And natural gas is now at a two-year low.

Henry Hub gas futures in New York are trading around $4.90 per million British Thermal Units, the first time gas contracts have been trading under $5 since September, 2006, and gas prices are now 64% off their summertime high.

Why has gas fallen so much? For pretty much the same reasons oil has fallen. Natural gas supplies are plentiful, for starters. The dismal economy is tamping down demand, especially among industrial users. More specifically, big stockpiles of natural-gas substitutes like heating oil are building, putting more pressure on gas prices even in the middle of winter.

Granted, natural gas still isn’t cheap by historical standards; it spent most of the 1990s between $2 and $3. And if past is prologue, it can rebound suddenly—natural gas prices doubled in the month following that 2006 trough.

But cheaper natural gas does put pressure on the economics of clean energy, especially wind power, which is already struggling with the fallout of the credit crunch.

If today’s lowish natural gas prices continue—it’s currently below the U.S. government’s official 2009 forecast—that will put an even greater onus on government policy to support clean energy. Most important will be the shape that government support takes, given Washington’s mixed track record of boosting renewable energy. More on that to come.