my %hash;
my $current_token = '';
while (<DATA>) {
    my ($token, $value ) = $_ =~ m/^([^\s]+)\s+(.*)/;
  next unless $token;
    if ( $token eq $current_token ) {
        ${$hash{$token}}[-1] .= ' ' . $value;
    } 
    else {
        $current_token = $token;
        push @{$hash{$token}}, $value;		
    }
}
use Data::Dumper;
print Dumper \%hash;

__DATA__
HEADER  Header 1 stuff
TITLE   Title 1 stuff
TITLE   2 more title 1 stuff
COMPND  complicated stuff 1
COMPND  2 continued complicated stuff 1
HEADER  Header 2 stuff
TITLE   Title 2 stuff
TITLE   2 more title 2 stuff
COMPND  complicated stuff 2
COMPND  2 continued complicated stuff 2
HEADER  Header 3 stuff
TITLE   Title 3 stuff
TITLE   2 more title 3 stuff
COMPND  complicated stuff 3
COMPND  2 continued complicated stuff 3
COMPND  3 continued complicated stuff 3
HEADER  Header 4 stuff
TITLE   Title 4 stuff
TITLE   2 more title 4 stuff
COMPND  complicated stuff 4
COMPND  2 continued complicated stuff 4
HEADER  Header 5 stuff
TITLE   Title 5 stuff
TITLE   2 more title 5 stuff
COMPND  complicated stuff 5
COMPND  2 continued complicated stuff 5
HEADER  Header 6 stuff
TITLE   Title 6 stuff
TITLE   2 more title 6 stuff
COMPND  complicated stuff 6
COMPND  2 continued complicated stuff 6

__END__
$VAR1 = {
          'HEADER' => [
                        'Header 1 stuff',
                        'Header 2 stuff',
                        'Header 3 stuff',
                        'Header 4 stuff',
                        'Header 5 stuff',
                        'Header 6 stuff'
                      ],
          'TITLE' => [
                       'Title 1 stuff 2 more title 1 stuff',
                       'Title 2 stuff 2 more title 2 stuff',
                       'Title 3 stuff 2 more title 3 stuff',
                       'Title 4 stuff 2 more title 4 stuff',
                       'Title 5 stuff 2 more title 5 stuff',
                       'Title 6 stuff 2 more title 6 stuff'
                     ],
          'COMPND' => [
                        'complicated stuff 1 2 continued complicated stuff 1',
                        'complicated stuff 2 2 continued complicated stuff 2',
                        'complicated stuff 3 2 continued complicated stuff 3 3 continued complicated stuff 3',
                        'complicated stuff 4 2 continued complicated stuff 4',
                        'complicated stuff 5 2 continued complicated stuff 5',
                        'complicated stuff 6 2 continued complicated stuff 6'
                      ]
        };