The WilderHill New Energy Global Innovation Index (NEX), a basket of 86 stocks in markets around the world, gained 39.7% last year, but was essentially flat in the fourth quarter. The NEX dropped 61% in 2008 and remains well below its November 2007 record.

Gains were uneven across the subsectors included in the index. The nine power storage stocks led the way, gaining 120%, on average, for the year. Standouts include BYD, an electric car and battery maker, which gained 439% on the Hong Kong Stock Exchange, and Maxwell Technologies, manufacturer of ultracapacitors, gained 252% on the Nasdaq.

The 17 energy efficiency stocks gained on average 48%, with Taiwan’s Epistar growing fastest, followed closely by EnerNOC and Cree, of the US, all of which turned in gains greater than 250%.

Solar and wind stocks in the index increased 30% and 36%, respectively, but some individual solar issues took a beating. Energy Conversion Devices was down 58% and Q-Cells shed 54% as the solar industry recorded its first year-over-year decline in demand.

The disparities among sub-sectors indicates that “shows that investors caught hold of new themes last year -- particularly the potential of advanced vehicle technologies and the smart grid,” says Michael Liebreich, chief executive of New Energy Finance, a partner in producing the index.

The universe of public clean tech companies expanded in 2009 and is poised to continue growing as companies pursue initial public offerings (IPOs).

There were 32 clean technology IPOs that brought in $4.7bn, according to data compiled by the Cleantech Group.

The NEX added to its mix advanced batter maker A123 Systems, which went public in the third quarter, raising $380m in one of the year’s highest-profile IPOs. Also new to the index was China Longyuan Electric Power Group, the wind company whose fourth-quarter floatation raised $2.23bn on the Hong Kong Stock Exchange, making it the largest IPO in the sector last year.

(The NEX also dropped from the index: BKW FMB Energie, a Swiss power company; Evergreen Solar, a photovoltaic manufacturer; Sharp, the Japenese electronics maker; Theolia, a French wind developer; and Umicore, a Belgian power storage compay.)

Asian issues dominated the 2009 clean tech IPO scene, garnering 72% of capital raised, according to Cleantech Group.

In December, two more clean energy companies – high-profile thin-film solar manufacturer Solyndra, and biofuels player Codexis – filed for IPOs.