you show
$hash{'mode'}{'component'} = [{'command' => 'cmd1'}, {'command' => 'cmd2'}];

simplist would be
$hash{'mode'}{'component'} = ['cmd1', 'cmd2'];

but I'd go for
$hash{'mode'}{'component'}{'commands'} = ['cmd1', 'cmd2'];


##</code><code>##

#!/perl -w
use Data::Dumper;
use strict;

my %hash;

my $current_comp = "";
my $current_mode = "";

my %the_hash;

while (<DATA>) {
	chomp;
	my ($coord,$data) = split /=>/;
	my ($row,$col) = split /,/, $coord;

	if ($col == 0) {
		$current_comp = $data;
		next;
	} 
	if ($col == 2) {
		$current_mode = $data;
		next;
	} 
	if ($col == 4) {
		push @{$the_hash{$current_mode}{$current_comp}{'commands'}}, $data;
		next;
	} 
}
print Dumper(\%the_hash);

##</code><code>##

push @{$the_hash{$current_mode}{$current_comp}{'commands'}}, $data;

##</code><code>##

$VAR1 = {
          'mode1' => {
                       'comp3' => {
                                    'commands' => [
                                                    'command1',
                                                    'command2'
                                                  ]
                                  },
                       'comp1' => {
                                    'commands' => [
                                                    'command1'
                                                  ]
                                  }
                     },
          'mode2' => {
                       'comp2' => {
                                    'commands' => [
                                                    'command1',
                                                    'command2',
                                                    ''
                                                  ]
                                  }
                     }
        };