I found this thread using google while I was trying to achieve this as well. I'm fully aware that it is very
old and I'm usually the one who states not to kick old threads but I like to post a solution that I found on the net.
ufraw-batch --wb=camera --exposure=0 --out-type=jpeg --compression=96 *.PEF
which will convert all pefs in a directory to jpegs with the same base filename; you can specify a different output directory using the --out-path option (useful when you shoot raw+jpeg).
The command above is slightly modified from http://jcornuz.wordpress.com/2007/10...verting-batch/
I have changed the --exposure option from auto to 0 as this will result in a jpeg that looks very similar to the original pef (it's slightly lighter, a tenth of a stop or so).
If Tom Brown is still around, he might want to mark this thread as solved.
A note: this worked for images from a K10D. It can theoretically work for newer cameras as well but might require a newer version of ufraw. It should also work for raw files from other brands like Canon and Nikon.