One of the few benefits of the financial slump of recent months has been the precipitous fall in energy prices. Consumers, who in the summer had been expecting to pay $4 a gallon for gasoline and diesel and $10 per million British thermal units (BTUs) for natural gas for the foreseeable future, are now readjusting to more-affordable prices.

But it's not just oil producers who are lamenting the sudden change in outlook. Companies investing in alternative energy sources also are facing a far more uncertain future—one that could have repercussions well beyond the green energy sector itself.

The problem is twofold:

• The big fall in prices of traditional energy sources—oil, coal and natural gas—has undercut one of the main rationales for switching to green energy. With oil at $70 or so a barrel,...