<form method="POST" action="sorgula.php">
   <input type="text" name="domain" placeholder="örn: alanadi" />
   <select id="tlds" name="tlds">
      <option value="top">En Çok Tercih Edilen</option>
      <option value="eu">Avrupa Domainleri</option>
      <option value="us">Bizim Önerilerimiz</option>
   </select>
<input type="checkbox" name="tld[]" id="com" value=".com" />
<input type="checkbox" name="tld[]" id="net" value=".net" />
<input type="checkbox" name="tld[]" id="org" value=".org" />
</form>

$(function(){
   $(" #tlds").change(function(){
       
     if($(this).val() == "top"){
        $("input:checkbox").each(function(){
       $(this).prop('checked', false);
       
      });
     $("#com,#net").prop('checked',true);
     }
       
   });
});