The clean energy industry is still in a fragile state, but for investors willing to seek out the best opportunities, this could be just as profitable as the tech industry was. Here are my picks for the best stocks in clean tech right now.

GT Solar (Nasdaq: SOLR)
The solar sector has been hurting so far in 2011, but that hasn't kept GT Solar from making its investors happy. So far this year, shares have climbed 78% on the back of new contracts for solar production equipment and a splashy entry into the LED market.

Most of the excitement has surrounded the company's new crystallization furnaces that have racked up $854.6 million in contracts since April. Some analysts are concerned that GT Solar will suffer a lack of demand in 2012 as solar manufacturers cut back on capacity additions but a more diversified line of products will help the company adjust.

Clean Energy Fuels (Nasdaq: CLNE)
In a few years, you may be watching natural gas prices more closely than oil prices to see what you'll be paying at the pump. That's because the natural gas fueling infrastructure is slowly but surely making its way to a neighborhood near you. When that happens, a natural gas vehicle will be a viable option for millions of drivers.

The natural gas revolution has already begun with buses and is quickly moving to trucking companies, and passenger vehicles will follow. The infrastructure is the groundwork the industry needs for natural gas vehicles and Clean Energy Fuels is at the forefront.

  • Click here to add Clean Energy Fuels to My Watchlist.

SunPower (Nasdaq: SPWRA)
And now for the pick that appears to have gone out of style recently: SunPower. The solar efficiency leader recently announced weaker-than-expected preliminary second-quarter results, which sent shares tumbling, but the long-term trends are still in the company's favor.

High-efficiency panels mean lower costs for land, inverter, and other development costs. As SunPower cuts cost, it will gain an advantage over competition. Lower cost suppliers like First Solar (Nasdaq: FSLR) may have less expensive panels, but it's the overall system costs that matter, and less efficient panels have higher balance of system costs. We are reaching an inflection point in the industry that will lead to some near-term financial pain, but long-term trends still favor the falling costs of solar energy.

Foolish bottom line
The clean tech industry is full of opportunities and landmines, so be careful to watch for risks and not just opportunities. A strong balance sheet can be just as important as a cool technology when the industry goes through ups and downs.

Track the performance of my picks on My CAPS page, where I have given each of these stocks an outperform rating.

Fool contributor Travis Hoium owns shares of First Solar and SunPower and has also sold put options in SunPower and GT Solar, whew. You can follow Travis on Twitter at @FlushDrawFool, check out his personal stock holdings or follow his CAPS picks at TMFFlushDraw.

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