May I recommend this for near-transparency:
convert 'yourfile.png' ppm:- | jpeg-recompress -t 97 -q veryhigh -a -m smallfry -s -r -S disable - yourfile.jpg
It uses imagemagick's convert
and jpeg-recompress
from jpeg-archive.
Both are open-source and work on Windows, Mac and Linux. You may want to tweak the options above for different quality expectations.