Three New England venture capitalists picked 1366 Technologies as the winner of a startup competition at a Greentech Media conference Wednesday.

The panel, made up of Jeff Andrews of Atlas Ventures, Rob Day of @Ventures and Jay Fiske of Massachusetts Green Energy Fund, named 1366 as the most promising of fivesolarstartups that presented their technologies and business plans at the conference. Aside from being named the top dog, the Lexington, Mass.-based startup also took home a hydrogen car. A toy version, that is.

Still, judges said 1366 Technologies faces some challenges. Andrews, a partner with Atlas Ventures, said he is concerned about the company’s ability to keep up with the rapidly falling prices of thin-film solar, for example.

“Modifying silicon is a tough train to be on,” he said. “A number of people … have been tolling the death knell of silicon.”

The contest, which took place at Greentech Media’s PV Annual 2008 conference near Boston, also provided the startups with the opportunity to disclose new deals and other news. Aside from 1366 Technologies, the other contestants were Cyrium Technologies, GreenVolts, Stion and SV Solar.

Founded only last fall, MIT-spinoff 1366 Technologies has focused on improving the design and manufacturing of multicrystalline solar cells so that they can capture more sunlight and generate more electricity, said Adam Lorenz, a founding member of the company.

The company, which raised $12.4 million in December from Polaris Venture Partners and North Bridge Venture Partners, will spend most of the money outfitting a fabrication line in Lexington, he said. Company employees have chipped in another $500,000.

1366 Technologies’ ultimate goal is to make solar generation as cheap as coal-based energy by 2013. Lorenz emphasized that the company isn’t developing a brand-new manufacturing technology. Instead, it’s bent on improving a process that could make solar energy widely affordable to the masses.

The company also has developed a wire that allows solar cells to capture more light, a technology that has been licensed to metal-product makers Ulbrich in Connecticut and Schlenk in Germany.

The firm also boasts some high-powered board members, including Bob Metcalfe, inventor of the Ethernet. The company plans to automate a 25-megawatt plant in 2009 and generate profit by 2011.

Meanwhile, Cyrium Technologies touted its quantum-dots technology, which it claims can boost the efficiency of concentrated photovoltaic cells. The startup, based in Ottawa, expects to generate revenue for the first time from its solar technology later this year. In fact, Stephen Eglash, who took over as CEO last December, is projecting revenue of more than $100 million in 2011 and double that in 2012.

Cyrium started its life as a fabless chip company, meaning it designed semiconductors and worked with a foundry to manufacture them. Several years ago, it began to develop solar cells for satellites. Now it builds earthbound solar farms.

The company hopes to dramatically reduce the amount of solar-cell material (by 500 to 1,000 times) by adding tiny quantum dots made of gallium arsenide to the middle layer of the solar cell. The materials can increase light absorption, which in turn enables each cell to generate mo re electricity.

Also at the conference, GreenVolts, another player in the high-concentration photovoltaic field, announced it is bidding for a 26-megawatt project that would ramp up to a capacity of 1,000 megawatts per year by 2015. But CEO Bob Cart played coy and wouldn’t divulge further details.

The three-year-old company, based in San Francisco, makes high-concentration photovoltaic systems it calls CarouSol. The system sits low on the ground and is capable of tracking sunlight.

Unlike other solar technologies, high-concentration solar systems can produce power more efficiently by using mirror and lenses to amplify the light’s intensity as it passes through solar cells. In some other solar-cell technologies, light can easily scatter and be lost before the energy-generation mechanism kicks in.

GreenVolts has raised $10 million and won a project to build a 2-megawatt power plant for PG&E, and it is bidding for a 26-megawatt project. The deal with PG&E would create the largest high-concentration solar farm in the United States, Cart said.

Another competitor, SV Solar, is developing a technology that uses a small prism to concentrate standard silicon-based solar cells, more than doubling their efficiency. The company plans to turn the low-concentration cells into a panel the same size and shape of traditional panels today, at a lower cost than those standard panels.

SV Solar claims it also has lower capital costs than traditional panels, anticipating factory costs of about $450,000 per megawatt of capacity. CEO Steven White hopes that advantage will help make the company attractive to investors.

The company expects to raise a second round of finding in the second half of this year, and to use to money to finance a 25-megawatt automatic production line in Germany and to develop its sales and distribution channels. The final startup in the competition plays in a different fields (See Stealthy Stion to Raise Another Round)

Stion claims its thin-film solar technology will be able to convert more sunlight into electricity than many traditional solar cells, which have higher efficiencies than thin films today, and to reach lower costs per watt than its competitors.