What applications allow the user to batch convert HTM files into PDF?
Try chaining up
html2ps (http://user.it.uu.se/~jan/html2ps.html) and
ps2pdf. Both are included in all major Linux distribution and are console utilites that you can use in shell scripts.
Personally, I use HTMLDOC for this. (Apart from the commandline, it also has a GUI and the option to have it run as a web service via CGI.) There are Windows, Linux, Mac OS X and Unix versions available. You can build your own executable, because the source is available via GPL.