This will do the trick in Perl:

use strict;
use warnings;

my @megaMotif = (
    [ "AGCT", "0", "370", "1" ],
    [ "AGGT", "3", "52",  "1" ],
    [ "TGAA", "2", "233", "0" ],
    [ "AGAG", "0", "32",  "0" ]
);

my @megaMotifSorted =
    sort { $a->[1] <=> $b->[1] || $a->[3] <=> $b->[3] }
    @megaMotif;
[download]

Please note the following two things:

1. The name of the language is "Perl", not "PERL".
2. When making your array, the outhernmost brackets should be parentheses "( ... )" and not square brackets "[ ... ]". Square brackets will make your list into an anonymous array rather than a normal array. In your version @megaMotif only contains one element, such as "ARRAY(some_hex_value)". Doing a sort on an array with only one element will not bring you very far.

   Did you just change the brackets in your posting or am I going mad? I could have sworn I just copied-and-pasted your code in my editor and the outernmost brackets were square and not round. If you did change them afterwards, make a little note of it otherwise it gets difficult to follow the discussion.