There are so many ways, you need to give more info about your system and constraints before a best one can be suggested. Just for starters:

• Lots of CPAN modules, for example ImageMagik, IPG's JPEG library, NetPBM, libpng (and that's just the older ones)
• Scipting in GIMP (in Perl of course) via the Gimp::Fu
• On Unix like boxes you can install the pbm/pnm software and control it with Perl
• On Windows boxes there are lots of graphics manipulation program that support scripting (I have an old version of CorelPaint that I sometimes use)

Do you just want BMP to JPG conversion? Do you need to resample images (change size or colour depth)? Do you need to control the output quality? What platform are you running on? Are you the sys admin?

It is certainly better to use Perl for this type of stuff but exactly how you use it depends on what you are trying to achieve