while ($line = <SH>){
        if($line =~ m/$agent/){
                $line = $collect;
#this line will be replaced by the $collect line in the file OUT

        } elsif ( $line =~ m/best1collect/) {
                next;
#this line will NOT appear in the file OUT, because you 
#don't reach the print command. If you want this line in
#the OUT file, I suggest, you use a continue block. See at
#the end.

        } elsif ($line =~ m/'syslogd'\)/){
                my $newline = $. + 3;
                $newline = $bgs;
                print OUT "$newline\n";
# this line will appear in the OUT file , but have the 
# bgs line inserted before.
        }
# all other lines will be copied.
     print OUT $line;
     print $line;
    }
[download]

Here is the version that does not omit lines. The statements in the continue block are executed always at the end of each loop.

   while ($line = <SH>){
        if($line =~ m/$agent/){
                $line = $collect;
        } elsif ( $line =~ m/best1collect/) {
                next;
        } elsif ($line =~ m/'syslogd'\)/){
                my $newline = $. + 3;
                $newline = $bgs;
                print OUT "$newline\n";
        }
    } continue {
     print OUT $line;
     print $line;
    }
[download]