The following is a quick and dirty reworking of your code to make it parse under strict and it also uses CGI.pm. It's not guaranteed to work, but if you can cobble it together, it's going to be much easier to maintain. In addition to the 'use CGI or die' post that was mentioned, you might want to read 'use strict' is not Perl to gain insight as to why I eliminated (most) of your global variables.

#!/usr/local/bin/perl -w
# Define Variables                                 #
use strict;
use CGI qw/:standard/;
my $basedir = '/home/mysite/www/';
my $baseurl = 'http://www.mysite.com/';
my @files = ('*.htm','*.html','*/*.html');
my $title = "The Silver Machine";
my $title_url = 'http://mysite.com/';
my $search_url = 'http://www.mysite.com/search.html';


# Done                                         #
######################################################################
+########

# Parse Form Search Information
# if it's a single form value, map the value as a scalar, other wise, 
+the value is
# and arrayref
my %FORM = map { $_, @{[ param($_) ]} > 1 ? [ param($_) ] : param($_) 
+} param();

# Get Files To Search Through
my $files = &get_files;

# Search the files
my ( $include, $titles ) = search( $files );

# Print Results of Search
return_html( $include, $titles );
    
sub get_files {
   my @FILES;
   chdir($basedir);
   foreach my $file (@files) {
      my $ls = `ls $file`;
      my @ls = split(/\s+/,$ls);
      foreach my $temp_file (@ls) {
         if (-d $file) {
            my $filename = "$file$temp_file";
            if (-T $filename) {
               push(@FILES,$filename);
            }
         } elsif (-T $temp_file) {
            push(@FILES,$temp_file);
         }
      }
   }
   return \@FILES;
}

sub search {
   my @FILES = @{$_[0]};
   my ( %include, %titles );
   my @terms = split(/\s+/, $FORM{'terms'});

   foreach my $FILE (@FILES) {

      my $string;
      open(FILE,"$FILE") or die "Can't open $FILE for reading: $!";
      {
          local $/;
        $string = <FILE>;
      }
      close(FILE);
      $string =~ s/\n//g;
      if ($FORM{'boolean'} eq 'AND') {
         foreach my $term (@terms) {
            if ($FORM{'case'} eq 'Insensitive') {
               if (!($string =~ /$term/i)) {
                  $include{$FILE} = 'no';
                  last;
               } else {
                  $include{$FILE} = 'yes';
               }
            } elsif ($FORM{'case'} eq 'Sensitive') {
               if (!($string =~ /$term/)) {
                  $include{$FILE} = 'no';
                  last;
               } else {
                  $include{$FILE} = 'yes';
               }
            }
         }
      } elsif ($FORM{'boolean'} eq 'OR') {
         foreach my $term (@terms) {
            if ($FORM{'case'} eq 'Insensitive') {
               if ($string =~ /$term/i) {
                  $include{$FILE} = 'yes';
                  last;
               } else {
                  $include{$FILE} = 'no';
               }
            } elsif ($FORM{'case'} eq 'Sensitive') {
               if ($string =~ /$term/) {
                  $include{$FILE} = 'yes';
                  last;
               } else {
                  $include{$FILE} = 'no';
               }
            }
         }
      }
      if ($string =~ /<title>(.*?)<\/title>/i) {
         $titles{$FILE} = "$1";
      } else {
         $titles{$FILE} = "$FILE";
      }
   }
   return ( \%include, \%titles );
}

sub return_html {
   my %include = %{$_[0]};
   my %titles  = %{$_[1]};
   open(FH,"../top.html") || die "couldn't open file $!\n";
   my @html=<FH>;
   close(FH);
   print @html;
   print "\n <center>\n  <h1>Search Results</h1>\n </center>\n";
   print "Here ya go, they're in no particular order:<p><hr size=7 wid
+th=75%><p>\n";
   print "<ul>\n";
   foreach my $key (keys %include) {
      if ($include{$key} eq 'yes') {
         print "<li class=bullets><span class=bullets><a href=\"$baseu
+rl$key\">$titles{$key}</a></span></li>\n";
      }
   }
   print "</ul>\n";
   print "\n";
   print "</ul><br><hr size=7 width=75%><P>\n";
   print "<ul>\n<li class=bullets><span class=bullets><a href=\"$searc
+h_url\">Back to Search Page</a></span></li>\n";
   print "<li class=bullets><span class=bullets><a href=\"$title_url\"
+>$title</a></span></li>\n";
   print "</ul>\n";
   print "<hr size=7 width=75%>\n";
   print "</body>\n</html>\n";
}
[download]

Cheers,
Ovid

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