The election last night of Barack Obama to the White House has many green investors cheering, but their elation may be short-lived. For one, the ROI of alternative energy is still pegged to the price of fossil fuels. Second, environmentalists may find themselves at cross-purposes with one faction leading the charge for a greener grid while the other seeks to protect endangered species and offshore territory from solar arrays and wind farms.

Perhaps the biggest green market, however, will not be an Obama-led green mandate, but emerging markets like China and India. In these places, green presents a true economic gain untethered from the price of oil, coal or natural gas.

That’s because the cost of pollution in these economies has a true impact on the GDP. Pollution raises the price of food, energy and health care. In the case of China, the pollution quotient adds enough overhead to make countries such as Vietnam, Pakistan and Thailand lower cost providers.

In India, the battle of a new Tata Motors plant for the company’s sub-micro thrifty car has forced a relocation that cost Tata millions.

Here in the U.S., though, a new era of subsidized green may lose its luster if fossil fuel prices stabilize at current levels – or even drop.

Green alternatives have always been pegged to the cost of doing business in a fossil-fuel economy. That’s why we saw so many solar IPOs soar with the ever-climbing price of oil. As oil prices retreated, so went the fortunes of so many solar investors.

This proves that self-righteousness is not a technical indicator or an incentive for long-term investments in the green sector. Self-righteousness is not the same as greed, which directly affects the climate for trading.

Now that the green movement has appropriated nuclear, we could see some distorted numbers creeping into the market as why alternative energy is more economically viable than two years ago.

But even the uranium industry doesn’t believe that, with the price of yellow cake down about half from a year ago.

For green stocks to truly perform, the American economy has to be resuscitated.

Over the long haul, green stocks will find themselves tied more to consumer spending than to government hand-outs. Once the economy is restored, and people start driving to the mall and vacation homes in the Outer Banks; once Americans stop conserving energy and turn up the heat in their homes to stay warm; and once alternative energy returns to a better economic alternative to fossil fuels — at that time we’ll see green stocks being to take off again.

Near term, green stocks could be a speculators playground as the Obama halo effect sends up prices. In the mean time, I’d still put my money in oil drillers.