Old world problems have caught up to New World growth here in the waning days of 2008. Just a few months ago, concepts like clean energy and energy independence were red hot. Today, projects–in fact whole companies focused on these challenges–are collapsing under the weight of sliding oil prices and extremely tight capital markets.

Former high-flyers such as SunPower (NSDW: SPWRA) are down more than 80 percent from their highs and are starting to look like value stocks. Smaller fare are in danger of disappearing entirely, including companies boasting first-rate technologies. And even large, financially solid utilities appear to be scaling back projects, at least for the time being. That’s despite the fact that more than half the states have now set legally enforceable targets for renewable energy use and the strong likelihood for a national standard shortly after the Obama administration takes office in January.

To be sure, the economy’s dire straits have probably put the brakes on legislation that would mandate a rapid conversion to clean energy. Even some of the proponents of rapidly phasing out coal as a power source are at least privately admitting that ramping up customer rates now is a non-starter, at least until the economy gets back on its feet.

The move to 21st century energy, however, is far from dead. For one thing, the Obama administration appears to be making infrastructure development–including construction of a 21st century quality power grid–a cornerstone of its plans to get the US economy out the ditch. And October’s omnibus financial system rescue package contained a large number of tax cuts and credits for clean energy as well, including, for the first time ever, carbon capture projects.

Government support also extends to the states. The most ambitious proposal to date comes from California Governor Arnold Schwarzenegger, who’s advocating a 33 percent renewable energy target for his state. Other states, including Michigan, are also increasingly supportive–again, as much from the perspective of creating jobs as from the desire to pursue the lofty goals of energy independence and reducing greenhouse gases.

Federal support means dollars are going to flow into this industry, no matter how bleak things get for the consumer. And even here, there’s reason to expect business won’t be nearly as bad as sector stock prices now reflect. Installations of solar panels on houses, for example, are still expected to grow 40 percent in 2009, according to many observers.

In the Nov. 20 Wall Street Journal, a columnist opined that planned reductions in US utility capital spending for 2009 as the harbinger of a deepening slump for clean energy, highlighting Duke Energy’s (NYSE: DUK) halving of a USD100 million investment to install solar panels for its Carolinas customers. That very day, however, Duke announced a wind energy partnership with Wal-Mart (NYSE: WMT) to supply up to 15 percent of that company’s power for its 360 stores and other facilities in Texas. That’s a much larger net commitment by Duke to clean energy, albeit a more focused one.

The clean energy companies that keep growing during these tough times will lead the boom when conditions improve. Wal-Mart’s financial power–demonstrated by its very strong third quarter earnings–ensures the Duke partnership will be adequately funded and that return on investment will be fair. I expect to see similar deals supplementing the already strong government commitment.

Of course, Duke itself is no slouch financially, a fact that clearly sets it apart from the small companies and venture capital outfits that have been its main rivals for projects to date. And it’s translating into a major competitive advantage for winning new contracts, as this financial and economic crisis has worsened.

The upshot for investors: Despite the current turmoil, the long-term clean energy boom is still very much alive. But only companies strong enough financially and operationally to weather current conditions will be left standing to enjoy it.

Those are of course the kind of companies New World 3.0 is building positions in now. As the Portfolio shows, we’ve sustained some losses, mainly because certain stocks we bought cheap in September and October have gotten cheaper still. The key, however, is for the underlying businesses to weather the storms. As long as that happens, today’s red ink will turn to black–probably a lot sooner than anyone suspects.

We’re studying clean energy companies in depth in On the Beat. My article, The Real Alternatives, focuses on the changing playing field for clean energy producers, highlighting new Portfolio addition AES Corp (NYSE: AES). Real Energy Editor Elliott Gue spotlights natural gas’ potential, focusing on extremely battered Chesapeake Energy (NYSE: CHK) in Energy: Complacency Breeds Opportunity. And Infratech Editor GS Early is taking a look at the smart grid and emerging technologies that enhance power transmission performance to reduce waste, pollution and the need to build more power plants.

Again, this market remains one of the toughest in memory. The close on Wednesday, Nov. 19, was the lowest in five years, and the breaking of 8,000 on the Dow Jones Industrial Average is a key psychological event in a market where negative emotions are running wild.

What you buy now could well go lower in the days following. But we’re playing for the long-term here, building positions in strong companies geared up to take advantage of what’s still set to be the biggest investment boom in decades. That means being patient and focused on the businesses when everyone else is reacting to exceptionally jagged lines on a price chart.