JavaFan's already answered your core question quite thoroughly, but I'd like to offer a little side advice on the true travesty1 in your demo code: 
$fileline =~ s/$line.shtml"-->/$line.shtml"-->\n<SCRIPT language="Java
+Script" SRC="http:\/\/mygreatwebsite.net\/cgi-bin\/gcountdir\/gcount.
+pl?0=$line"> <\/SCRIPT>/

[download]
Although / is the default regex delimiter in Perl, you can use different punctuation in that role to avoid "leaning toothpick syndrome": 
$fileline =~ s#$line.shtml"-->#$line.shtml"-->\n<SCRIPT language="Java
+Script" SRC="http://mygreatwebsite.net/cgi-bin/gcountdir/gcount.pl?0=
+$line"> </SCRIPT>#

[download]
or even, if you want to get fancy: 
$fileline =~ s[$line.shtml"-->]
              [$line.shtml"-->\n<SCRIPT language="JavaScript" SRC="htt
+p://mygreatwebsite.net/cgi-bin/gcountdir/gcount.pl?0=$line"> </SCRIPT
+>]

[download]

Edit: 1Just to clarify, I referred to the regex in question as a "travesty" solely to echo the OP's description of the code it came from as "the below travesty". I would not normally consider it nearly bad enough to qualify as such.

In reply to Re: What's the deal with apostrophes? by dsheroh
in thread What's the deal with apostrophes? by tallCoolOne

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