Good question, there aren't exactly any good tools that interweave several languages into the same environment. Not just for php-mysql but also for php-html or html-javascript or php-javascript. Phpstorm gives you intellisense for sql-strings embedded in your php code but that's the most advanced cross-language-feature i've seen, except for LINQ in C#.

Imagine a tool that could analyze this:

  //sql table T having columns int x, string y

  //php
  $data = sql_fetch_from_column(T)

  //javascript
  var d = <?=json_encode($data)?>
  for(a in d)
      var b = a.x / a.y;  //Type error, int division by string not defined