I think your immediate problem is not to do with regular expression matching or shell escape. Your immediate problem is because you are trying to replace the matching pattern with '$1' as an exact string, not as a back reference. Try this instead...

#!/usr/bin/perl -w

my $searchExp = $ARGV[0];
my $replaceExp = $ARGV[1];
my $textIn = <STDIN>;
my $count = 0;

# Do the replacing

eval "\$count = (\$textIn =~ s/$searchExp/$replaceExp/go)";

if ($count > 0) {
   print $textIn;
}

exit;
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And the output is exactly as expected...

>> echo 'JHTML `Java in here` code' | perl p11.pl '`(.*)`' '<%=$1%>'

JHTML <%=Java in here%> code
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