sub html_to_pdf
{
    my($pdffile,$htmlfile)=@_;
    
    $command = "htmldoc --webpage -f \"$pdffile\" \"$htmlfile\"";
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(General recommendation) please (do a favour to yourself and)

use strict;
use warnings;
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As a side note you can use alternate delimiters:

my $command = qq|htmldoc --webpage -f "$pdffile" "$htmlfile"|;
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is quite more readable IMHO. But then I would recommend you to use the list form of system which has the advantage of avoiding passing through the shell, which in turn you don't seem to need.

    print $command."\n";
    eval{system("$command");};
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You plainly don't need eval. The actual call may fail, but the system command may well succeed. It is its return value, along with $?, that you have to check.