Currently I use this strategy:
After submitting a HTML form or data sent using jQuery's $.get() or $.post() I need to know what is come and then apply logic on the basis of that.
suppose, I've got $_POST['username'], $_POST['password'] and $_POST['login_submit_button'].
In my processing script file, I do like this:
if(isset($_POST['login_submit_button']) && isset($_POST['username']) && $_POST['username'] != "" && isset($_POST['password']) && $_POST['password'] != "") {
  // calling a common function safe_vars() which does
  // mysql_real_escape_string(stripslashes(trim($any_variable_need_to_become_safe)))
  // and now using the above variables for different purposes like
  // calculation, insertion/updating old values in database etc.
}
I know all this logic is wrong or having serious issues, so I want a much-secure and perfect solution instead of this. I welcome to find out vulnerabilities and severe security-bleaches in my strategy. This question can help others too, if answers came more explanatory, this can be informative community wiki.
 
     
     
    