system("diff -q \"$File::Find::name\" \"$other_file\" > NU
+L");
if($?) {
    print "$file is different\n";
}
[download]

could be simplified to

if(qx/diff -q "$File::Find::name" "$other_file"/) {
    print "$file is different\n";
}
[download]

Update: Added quotes around file name variables to handle file names with spaces in them (thanks ikegami).