Is a PhD the highest degree?

It depends highly on your university and national system. The Doctor of Science title has already been cited by Dan C, and several European countries have a higher diploma called habilitation.

At the risk of answering a question that the OP may not actually be asking....

One of the biggest myths to deprogram grad students of is the idea that the Ph.D is "the highest degree" or is in fact in a well-defined ordering relationship with other degrees. It is true that a Ph.D will typically require other degrees as a prerequisite, and it is also true that (as far as I know) no degree program requires a Ph.D for admission. However, there's no useful sense in which the Ph.D is "highest" in anything. It is a certification that you can do research, and is almost always a mandatory step before getting a research position in academia.

But by that logic, an MBA, a J.D or an MD are also "highest" degrees.

The degree you're looking for (at least in the sciences) is called "Doctor of Science" and you can read all about it on Wikipedia:

Doctor of Science

Edit: As aeismail noted: Sometimes this degree is considered equivalent to a PhD and sometimes it's considered beyond a PhD. This distinction typically varies by country (all this is listed on the Wikipedia page).