my @flags = ();

while (<DATA>) {
    push @flags, /(-D\S+)/g;
}

use Data::Dump qw(dump);
print dump(\@flags);

__DATA__
     -D__c_plusplus=1 -D__cplusplus=1 \
     -D__NAMESPACES -D__STANDARD_CXX \
     -D__ghs -Dghs -D__SoftwareFloat \
     -D__m68k -Dm68k -D__mc68000 \
     -D__m68ec060 -Dm68ec060 

__END__

Result:
[
  "-D__c_plusplus=1",
  "-D__cplusplus=1",
  "-D__NAMESPACES",
  "-D__STANDARD_CXX",
  "-D__ghs",
  "-Dghs",
  "-D__SoftwareFloat",
  "-D__m68k",
  "-Dm68k",
  "-D__mc68000",
  "-D__m68ec060",
  "-Dm68ec060",
]