"@QUERY:FOO"
...data...
...data...
...etc...
"@ENDQUERY"
"@QUERY:BAR"
...data...
...data...
...etc...
"@ENDQUERY"

##</code><code>##

while (<FH>) {
    if ($_ =~ /^\"\@QUERY:(.*)\"/) {
        my $query = $1;
        my $i = 1;
        while (<FH> !~ /^\"\@ENDQUERY\"/) {
            print $_;
            #$data{$query}->{$i}->{$_} unless ($_ eq "");
            $i++;
        }
    }
}

##</code><code>##

Using perl 5.6.1 unless otherwise noted.
Apache 1.3.27 unless otherwise noted.
Redhat 7.1 unless otherwise noted.