The U.S. Department of Energy is doling out $41.9 million to 13 companies to develop and deploy fuel cells, which have largely been relegated to military use.

The grant winners include GENCO, Polyfuel, Plug PowerMTI MicroFuel Cells and ReliOn. The money will come from the stimulus funds. Naturally, the goal here is not just to encourage greentech development, but to create manufacturing and other types of jobs as well.

Fuel cells promise to provide green energy storage for everything from electronic gadgets to cars, but getting the right chemistry and keeping the manufacturing costs low are tricky to do. Many fuel cell companies rely on government research contracts to stay in business. Protonex Technology recently announced a $1.48 million contract from the U.S. Army to develop a solid oxide fuel cell that can run on different kinds of fuels, including biodiesel and butanol.

Fuel cell companies have found some success deploying their products for back-up power systems and industrial equipment such as forklifts, the DOE said. So the government is using the $41.9 million to support those uses.

ReliOn in Spokane, Wash., for example, is getting $8.6 million to deploy 180 fuel cells to provide backup power to AT&T’s wireless network in California. Sprint Communications, based in Reston, Va., is getting $7.3 million to set up backup power systems for its own telecom network. MTI MicroFuel Cells in Albany, N.Y., plans to use its $2.4 million to demonstrate a fuel cell developed for consumer electronics.

Latham, N.Y.-based Plug Power, which has been selling fuel cell packs for forklifts, is getting two grants. It plans to use the first grant ($3.4 million) to carry out a three-year project to demonstrate the use of its 5-kilowatt system to replace conventional furnaces and boilers to provide electricity and heat for residential and business use in California. It will use the second grant ($2.7 million) to install rack-mounted systems for emergency backup power.

Anheuser-Busch in St. Louis will use the $1.1 million to install 23 fuel cell packs in its fleet of forklifts in Fort Collins, Colo. Those forklifts have been using lead-acid batteries.

The 13 grant recipients are expected to contribute $72.4 million of their own funds to match the DOE grants.