First go get UFRaw, a OSS utility for manipulating images from digital cameras.  You can get it here:

http://ufraw.sourceforge.net/

Then just open up your command prompt and run something like:

c:\Data\PicsBeHere>"c:\program files (x86)\UFRaw\bin\ufraw-batch.exe" --out-type=jpeg --out-path=. ./*.cr2