Try this:

use strict;
use warnings;

my %biggest;

while ( <DATA> ) {
  chomp;
  my @items = split /,/;
  my $coords = join ',', @items[ 0 .. 2 ];
  my ( $time, $mag ) = @items[ 3, 4 ];
  if ( not defined $biggest{$coords} or $mag > $biggest{$coords}->[1] 
+) {
    $biggest{$coords} = [ $time, $mag ];
  }
}

for my $coords ( keys %biggest ) {
  print join( ',', $coords, join',', @{ $biggest{$coords}} ), "\n";
}


__DATA__
2550,531,66,10-12-2007 07:03:08.069,2
2549,529,62,10-12-2007 07:03:08.151,1
2550,531,66,10-12-2007 07:03:09.069,1
2549,529,62,10-12-2007 07:03:09.151,2
2550,531,66,10-12-2007 07:03:10.001,6
2550,531,66,10-12-2007 07:03:11.099,7
[download]

Output:

2550,531,66,10-12-2007 07:03:11.099,7
2549,529,62,10-12-2007 07:03:09.151,2
[download]